SIGSEGV: Illegal storage access. (Attempt to read from nil?) #27

snashraf · 2019-04-24T10:25:27Z

Hi Brent,

I am trying to run the latest slivar version: 0.1.1 via a shell script. I am getting below error.
54 samples matched in VCF and PED to be evaluated
SIGSEGV: Illegal storage access. (Attempt to read from nil?)
slivar version: 0.1.1

When I am trying to run the same script with Version 0.0.5, I am not getting any error.

Do you have any idea that what I am getting this error?

Thanks
Najeeb

brentp · 2019-04-24T13:05:56Z

can you show the command you are running? make sure you don't have repeated labels like:

--trio abc:some_expression ...
--trio abc:some_other_expression...

brentp · 2019-04-26T13:37:14Z

Hi Najeeb, I'd like to get this resolved, can you give more information?

snashraf · 2019-04-26T15:32:23Z

Hi Brent ,

Extremely Sorry for late reply !!
Please find the attached script. and I am trying to run this as.
slivar.txt

sh slivar.sh 54Samplesvcf2db.vcf.gz batch5.ped missinginped

brentp · 2019-04-26T16:17:30Z

would you try runnng the command using this binary (just gunzip and chmod +x) so we can see more debug info?
slivar_debug.gz

snashraf · 2019-04-28T10:09:48Z

54 samples matched in VCF and PED to be evaluated Traceback (most recent call last) slivar.nim(200) slivar slivar.nim(197) main slivar.nim(105) expr_main gnotate.nim(71) open zipfiles.nim(194) extractFile zipfiles.nim(182) extractFile streams.nim(88) readData SIGSEGV: Illegal storage access. (Attempt to read from nil?) slivar version: 0.1.2 54 samples matched in VCF and PED to be evaluated Traceback (most recent call last) slivar.nim(200) slivar slivar.nim(197) main slivar.nim(105) expr_main gnotate.nim(71) open zipfiles.nim(194) extractFile zipfiles.nim(182) extractFile streams.nim(88) readData SIGSEGV: Illegal storage access. (Attempt to read from nil?)

…

On Fri, Apr 26, 2019 at 7:17 PM Brent Pedersen ***@***.***> wrote: would you try runnng the command using this binary (just gunzip and chmod +x) so we can see more debug info? slivar_debug.gz <https://github.com/brentp/slivar/files/3122143/slivar_debug.gz> — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#27 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABBFINYPDWZPES4VD5P3AD3PSMTJVANCNFSM4HICPXHA> .

-- Syed Najeeb Ashraf

brentp · 2019-04-28T13:20:53Z

ok. that's easy. You got a zip file from an old release. If you get one linked from the latest release here: https://github.com/brentp/slivar/releases you'll be fine. Sorry for the trouble.

brentp · 2019-04-28T20:02:43Z

to clarify, by that, I mean grab the latest gnomad zip (GRCh37)

snashraf · 2019-04-29T07:07:09Z

Hi Brent,

Now I am getting below error.

slivar version: 0.1.2

54 samples matched in VCF and PED to be evaluated
[slivar] message for /gpfs/projects/bioinfo/najeeb/playGround/slivar/gnomad.hg37.zip:

gnomad hg37 v2.1
[slivar] evaluating on 22 trios
[slivar] 10000 1:1223697 evaluated 10000 variants in 56.9 seconds (175.8/second)
[slivar] 20000 1:2283207 evaluated 10000 variants in 42.5 seconds (235.1/second)
slivar.nim(200) slivar
slivar.nim(197) main
evaluator.nim(551) expr_main
evaluator.nim(401) set_infos
vcf.nim(283) get
system.nim(3059) sysFatal
Error: unhandled exception: index 0 not in 0 .. -1 [IndexError]
slivar version: 0.1.2

brentp · 2019-04-29T13:49:52Z

Hi Najeeb, sorry for the trouble. Can you share a small part of the VCF that I can use to recreate the error?

And do you get this with the original binary that you downloaded (or only the debug binary)?

I can't see anything obvious to change just yet.

genomics-geek · 2019-09-24T21:13:13Z

@brentp - I also come across this error SIGSEGV: Illegal storage access. (Attempt to read from nil?) occasionally.

Not sure exactly why it happens, but seems to not like VCFs coming from GATK CombineVariants or after using slivar and using the --regions with a BED file to filter.

genomics-geek · 2019-09-24T21:18:45Z

if I remove all the #GATKCommandLine. lines from the VCF header the error SIGSEGV: Illegal storage access. (Attempt to read from nil?) goes away just FYI

This is needed to remove GATK.CommandLine from VCF header. slivar errors out when these are present. See: brentp/slivar#27 (comment)

brentp · 2019-09-24T21:42:39Z

can you give me a small VCF to recreate?

genomics-geek · 2019-09-24T22:08:46Z

Yup here here is an example VCF
test.vcf.gz

brentp · 2019-09-24T22:15:00Z

thank you. how can I see the problem. I tried:

slivar_static expr --info "INFO.DP > 20" -v ~/Downloads/test.vcf.gz  > /dev/null

without problem.

genomics-geek · 2019-09-24T22:18:05Z

slivar expr --pass-only --vcf test.vcf --ped ped gives me the error.

PED file:

#family	kid	dad	mom	sex	disease
F000016986	sample2	NA	NA	female	unaffected
F000016986	sample1	NA	NA	male	unaffected
F000016986	sample3	sample1	sample2	male	affected

genomics-geek · 2019-09-24T22:20:19Z

I used version 0.1.6.

brentp · 2019-09-24T22:26:05Z

if I put that in x.ped:

$ slivar_static expr --pass-only --vcf ~/Downloads/test.vcf.gz --ped x.ped > /dev/null 
slivar version: 0.1.6 a135a8703f055b1b9a08632ce0d8887f174e7787
[pedfile] paternal_id: "NA" referenced for sample "sample2" not found
[pedfile] maternal_id: "NA" referenced for sample "sample2" not found
[pedfile] paternal_id: "NA" referenced for sample "sample1" not found
[pedfile] maternal_id: "NA" referenced for sample "sample1" not found
[slivar] 3 samples matched in VCF and PED to be evaluated
[slivar] Finished. evaluated 4 total variants and wrote 4 variants that passed your slivar expressions.

so, I'm not able to recreate.

genomics-geek · 2019-09-24T22:33:27Z

that's odd, I get:

[svcdgdbfx@l-0-01 execution]$ /mnt/isilon/dgd_public/clin-air/v2.0.0/tools/slivar/0.1.6/slivar expr --vcf test.vcf --ped ped 
slivar version: 0.1.6 a135a8703f055b1b9a08632ce0d8887f174e7787
[pedfile] paternal_id: "NA" referenced for sample "sample2" not found
[pedfile] maternal_id: "NA" referenced for sample "sample2" not found
[pedfile] paternal_id: "NA" referenced for sample "sample1" not found
[pedfile] maternal_id: "NA" referenced for sample "sample1" not found
[slivar] 3 samples matched in VCF and PED to be evaluated
SIGSEGV: Illegal storage access. (Attempt to read from nil?)
[svcdgdbfx@l-0-01 execution]$

brentp · 2019-09-24T22:34:21Z

what is your test.vcf?

genomics-geek · 2019-09-24T22:34:30Z

well, when it is uncompressed I get the error. I had to bgzip it when I uploaded to github haha.

brentp · 2019-09-24T22:35:30Z

oh. wow. I get the error on the uncompressed, but not compressed. will fix.

brentp · 2019-09-24T22:36:11Z

actually, this is already fixed in my dev branch will be out in next release. thanks for reporting.

genomics-geek · 2019-09-24T22:37:38Z

Thank you! Yea it was helpful to try to figure out why it was happening. What eventually fixed it for me was to compress VCF or to remove GATKCommandLine.

This is needed to remove GATK.CommandLine from VCF header. slivar errors out when these are present. See: brentp/slivar#27 (comment)

Tayazseven · 2020-09-01T21:00:11Z

@brentp Hi Brent, Following up on this issue. We are using slivar v0.1.10 and see this issue.

> slivar version: 0.1.10 917aa1a61bd0c0ba50521ea4146a3a4dc45b8b64
[pedfile] paternal_id: "NA" referenced for sample "F000073286_DGD-20-4514_WESTRIO_M" not found
[pedfile] maternal_id: "NA" referenced for sample "F000073286_DGD-20-4514_WESTRIO_M" not found
[pedfile] paternal_id: "NA" referenced for sample "F000073286_DGD-20-4516_WESTRIO_F" not found
[pedfile] maternal_id: "NA" referenced for sample "F000073286_DGD-20-4516_WESTRIO_F" not found
[slivar] 3 samples matched in VCF and PED to be evaluated
SIGSEGV: Illegal storage access. (Attempt to read from nil?)

But the thing is, I cannot recreate this issue since whenever I run it again, it passes through. We pass compressed vcf to slivar expr Do you have any suggestions?
My resource allocation:

cpu: 1 
mem: 12

brentp · 2020-09-01T21:26:17Z

can you share a small vcf and ped to recreate? you can try replacing "NA" with "0" or "-9" since those are accepted missing values in a pedigree file.

brentp · 2020-09-01T22:13:02Z

@Tayazseven can you make sure you have latest release (version 0.1.12).

brentp · 2021-03-10T06:00:00Z

@Phillip-a-richmond can you link a VCF with a RefCall variant that does have this problem?

Phillip-a-richmond · 2021-03-10T19:25:34Z

Okay so while trying to isolate the issue to the RefCall, I was unsuccessful. It turns out the issue that I solved with my zgrep for RefCall, was actually just because I uncompressed from vcf.gz to plain text, and then reran the slivar command on the uncompressed VCF.

If I had to say where the issue is exactly, my guess is that it has something to do with the bgzipped VCF I'm using being read into slivar.

So what I can reproduce with my files:

#SLIVAR 
$SLIVAR/slivar.exe expr --vcf Test_bcftoolsnorm.bcftoolsfilter.10000.vcf.gz \
    --ped Test.ped \
    --pass-only \
    -g $SLIVAR/gnomad.hg38.genomes.v3.fix.zip \
    --info "INFO.gnomad_popmax_af < $AF_CUTOFF && INFO.gnomad_nhomalt < $HOM_ALT_CUTOFF && variant.FILTER == \"PASS\" && variant.ALT[0] != \"*\"" \
    --js $SLIVAR/slivar/js/slivar-functions.js \
    -o $INVCF_NORM_FILTER_SLIVARRARE

Error:

> slivar version: 0.2.1 ceb97b26cd39d341dd7aa96ddb42239692df5b50
[slivar] 3 samples matched in VCF and PED to be evaluated
[slivar] message for /mnt/common/Precision/Slivar//gnomad.hg38.genomes.v3.fix.zip:
   > created on:2019-11-15
SIGSEGV: Illegal storage access. (Attempt to read from nil?)

But this code does not give an error:

#SLIVAR 
$SLIVAR/slivar.exe expr --vcf EPGEN055_bcftoolsnorm.bcftoolsfilter.10000.vcf \
    --ped Test.ped \
    --pass-only \
    -g $SLIVAR/gnomad.hg38.genomes.v3.fix.zip \
    --info "INFO.gnomad_popmax_af < $AF_CUTOFF && INFO.gnomad_nhomalt < $HOM_ALT_CUTOFF && variant.FILTER == \"PASS\" && variant.ALT[0] != \"*\"" \
    --js $SLIVAR/slivar/js/slivar-functions.js \
    -o $INVCF_NORM_FILTER_SLIVARRARE

I'm attaching here the uncompressed and compressed VCFs, with least 10000 lines in each of them. Hopefully that can help your debugging process.

Note, change the vcf.txt back to just vcf...github won't let me paste .

brentp · 2021-03-10T19:49:49Z

thanks very much @Phillip-a-richmond , I will have a look.

fakedrtom · 2021-03-12T20:26:55Z

Not sure if it is for the same reasons, but I have a VCF that is generating the same error that I could point you to if that would be helpful.

brentp · 2021-03-14T20:01:53Z

I can get this with the last release. With dev version, it seems to be fixed--though I'm not sure which change is to blame/praise for that.
@Phillip-a-richmond and @fakedrtom and anyone else who has had this issue, would you try the attached binary (should show v0.2.2 when run) and verify that the problem is resolved?

If so, I'll make a new release soon. Thanks.

brentp · 2021-03-14T20:02:31Z

... and now with the binary attached.

slivar.gz

Phillip-a-richmond · 2021-03-16T17:46:33Z

That binary didn't fix the problem for me.

> slivar version: 0.2.2 0401ef029e3b2dee542c56c35d1dae3a8c245dfb
[slivar] 3 samples matched in VCF and PED to be evaluated
[slivar] message for /mnt/common/Precision/Slivar//gnomad.hg38.genomes.v3.fix.zip:
   > created on:2019-11-15
SIGSEGV: Illegal storage access. (Attempt to read from nil?)

The VCF is bgzip'd with tabix 1.10.2 and indexed.

On the uncompressed VCF:

> slivar version: 0.2.2 0401ef029e3b2dee542c56c35d1dae3a8c245dfb
[slivar] 3 samples matched in VCF and PED to be evaluated
[slivar] message for /mnt/common/Precision/Slivar//gnomad.hg38.genomes.v3.fix.zip:
   > created on:2019-11-15
[slivar] Finished. evaluated 9785 total variants and wrote 23 variants that passed your slivar expressions.

Is there a verbose/debug option you've got working on a binary you can share? Perhaps we can pinpoint where the complaint is on my end?

Cheers,
-Phil

brentp · 2021-03-16T17:59:45Z

@Phillip-a-richmond , can you give the command that generates the error with the files that you posted above?

raungar · 2021-06-23T23:32:30Z

Hi-

Has this problem been solved? I am trying to implement slivar for patient data, so unfortunately I cannot share any VCFs. I have tried both with unzipped and bgzipped files, the most recent build, and the binary shared above.

I get this error after passing my vcf through bcftools csq

Thanks,
Rachel

Phillip-a-richmond · 2021-06-24T00:12:29Z

I may have dropped the ball on this one. Raungar the error went away for me when I cut out the RefCall lines from my VCF. Below is a functional pipeline starting with a merged VCF from deeptrio-->glnexus-->bcftools (merged.vcf.gz)

INVCF=${SAMPLE}.merged.vcf.gz
INVCF_NORM=${SAMPLE}_bcftoolsnorm.vcf.gz
INVCF_NORM_FILTER=${SAMPLE}_bcftoolsnorm.bcftoolsfilter.vcf.gz
INVCF_NORM_FILTER_NOREFCALL=${SAMPLE}_bcftoolsnorm.bcftoolsfilter.NoRefCall.vcf.gz
INVCF_NORM_FILTER_NOREFCALL_SLIVARRARE=${SAMPLE}_bcftoolsnorm.bcftoolsfilter.NoRefCall.slivarrare.vcf.gz

# Cutoffs
HOM_ALT_CUTOFF=15
AF_CUTOFF=0.001

# Step 1 - BCFTools normalize & apply filter
# BCFTOOLS
# Normalize VCF
$BCFTOOLS norm \
	-f $GENOME_DIR/$GENOME_FASTA \
	--threads @NSLOTS \
	-m - \
	-O z \
	--output $INVCF_NORM \
	$INVCF 

$TABIX -f $INVCF_NORM

# Filter normalized VCF for high depth + low alt allele support (soft-filter)
$BCFTOOLS filter \
         --include 'FORMAT/AD[*:1]>=5 && FORMAT/DP[*] < 600' \
         -m + \
         -s + \
         -O z \
         --output $INVCF_NORM_FILTER \
         $INVCF_NORM

$TABIX -f $INVCF_NORM_FILTER

# Step 2 - Get rid of RefCall from DeepVariant output
zgrep -v "RefCall" $INVCF_NORM_FILTER | bgzip -c > $INVCF_NORM_FILTER_NOREFCALL
tabix $INVCF_NORM_FILTER_NOREFCALL

# Step 3 - Slivar filter for gnomad frequency, here set to GRCh38
#SLIVAR 
$SLIVAR/slivar.exe expr --vcf $INVCF_NORM_FILTER_NOREFCALL \
    --ped $PED \
    --pass-only \
    -g $SLIVAR/gnomad.hg38.genomes.v3.fix.zip \
    --info "INFO.gnomad_popmax_af < $AF_CUTOFF && INFO.gnomad_nhomalt < $HOM_ALT_CUTOFF && variant.FILTER == \"PASS\" && variant.ALT[0] != \"*\"" \
    --js $SLIVAR/slivar/js/slivar-functions.js \
    -o $INVCF_NORM_FILTER_NOREFCALL_SLIVARRARE

I recommend grabbing an open source trio to share your errors. Plenty available, but I test with this one:

############
# EUROPEAN #
############
## HG01771 - Family IBS049 - EUR - IBS - FATHER 
wget -c -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR195/009/ERR1955499/ERR1955499_1.fastq.gz
wget -c -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR195/009/ERR1955499/ERR1955499_2.fastq.gz
## HG01770 - Family IBS049 - EUR - IBS - MOTHER
wget -c -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR195/005/ERR1955435/ERR1955435_1.fastq.gz
wget -c -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR195/005/ERR1955435/ERR1955435_2.fastq.gz
##  HG01772 - Family IBS049 - EUR - IBS - PROBAND (F)
wget -c -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR230/005/ERR2304565/ERR2304565_1.fastq.gz
wget -c -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR230/005/ERR2304565/ERR2304565_2.fastq.gz

brentp · 2021-06-24T06:56:18Z

Hi @raungar , I'd like to get this resolved, but I have not been able to recreate. Can you try running the same command with this binary attached and let me know what the full output is?

@Phillip-a-richmond if you can show me how to recreate, I'll look into it. Those header lines should not affect slivar. I am curious what a few of the RefCall lines look like so if you can paste those perhaps that will also give a clue.

brentp · 2021-06-24T06:57:37Z

@raungar binary attached this time:
slivar_debug.gz

(just download, gunzip, chmod +x slivar_debug, thne use slivar_debug instead of slivar).

brentp · 2021-06-24T07:11:11Z

I think I found the problem. Would you try this binary as well?
slivar_debug_fix.gz

JakeHagen · 2021-06-24T16:09:55Z

Hi Brent and everyone,

I believe I am having the same issue. First, those two binaries that you just posted did not solve the issue for me. But I do have some info that might help.

Oddly this error will occur most of the time, but when repeatedly trying the command, it will rarely run successfully (maybe 10% of the time).

For me at least, removing the RNC format field from glnexus VCFs seems to fix the error. From what I can tell the RNC format field does not follow the VCF spec.
Are we all trying on glnexus vcfs?

Attached are vcfs created using glnexus "get started page" and then removed the FORMAT/RNC

dv_1000G_ALDH2.vcf.gz
dv_1000G_ALDH2.rmRNC.vcf.gz

brentp · 2021-06-24T16:56:16Z

@JakeHagen ok. this is a great start. Now, can you share a command that generates the sigsegv?
I tried:

slivar_debug_fix expr -o x.vcf -v ~/Downloads/dv_1000G_ALDH2.vcf.gz --sample-expr "s:sample.AD[0] > 1" --alias <(echo "")

but it completes without issue (though it does give warning about multiallelics)

brentp · 2021-06-24T17:03:36Z

The RNC field is valid VCF so something else is going on. If I can recreate the bug then I should be able to fix, but I don't see it yet.
@JakeHagen does the slivar_debug_fix above resolve the issue for you?

raungar · 2021-06-24T17:25:39Z

Hi-

I figured out the problem for my VCF at least. This was purely a header issue for me -- I didn't have all the FORMAT tags in my header, which gave warnings but no errors. Adding in the proper FORMAT tags (ex: ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">) solved this problem for me.

Thanks,
Rachel

JakeHagen · 2021-06-24T18:42:52Z

@brentp Hi Brent, the command you used above works fine for me. Below is the command that errors for me.

./slivar_debug_fix expr -v glnexus/dv_1000G_ALDH2.vcf.gz --gnotate tmp/gnomad.hg38.genomes.v3.fix.zip | bgzip -c > t.vcf.gz

[slivar] 2504 samples matched in VCF and PED to be evaluated
[slivar] message for tmp/gnomad.hg38.genomes.v3.fix.zip:
   > created on:2019-11-15
Traceback (most recent call last)
/home/brentp/src/slivar/src/slivar.nim(249) slivar
/home/brentp/src/slivar/src/slivar.nim(246) main
/home/brentp/src/slivar/src/slivar.nim(110) expr_main
/home/brentp/src/slivar/src/slivarpkg/evaluator.nim(443) id2names
SIGSEGV: Illegal storage access. (Attempt to read from nil?)

The error usually only comes up when using --gnotate

JakeHagen · 2021-06-24T19:01:23Z

Also, now that you confirmed RNC is valid (wasn't familiar with character fields), I tried removing other format fields.
I have tried removing DP, and AD, and both times the above command works. So I really don't know what is happening.

brentp · 2021-06-24T20:42:23Z

I can recreate with the command above. I will have a fix out in next release soon. Thanks for the example @JakeHagen

JakeHagen · 2021-06-25T15:35:30Z

Thats great, thank you

brentp · 2021-06-25T16:20:00Z

OK. I have the fix in for this. Will add test and commit this weekend. Meanwhile, here is the binary. If you could verify that it works for you that would be great. I expect I can get a release out Sunday or Monday. Thanks so much for reporting everyone and for providing the test-case @JakeHagen , that is critical.
slivar_really_fix.gz

This is a debug binary so will be slow, but should work for the cases this issue is referencing.

JakeHagen · 2021-06-25T16:42:08Z

Yep that seems to do the trick. Thanks a lot for this.

brentp · 2021-06-28T10:02:39Z

this is finally, fully fixed in v0.2.4

mvelinder · 2022-04-14T18:17:10Z

Hey @brentp I'm running into this error again I think, only when using compound-hets. Here's what I'm running...

slivar_static compound-hets -v A1257-220114-VAR-Botto-Leukodystrophy_Final_1642265647.vcf.gz.slivarch.vcf.gz --skip NONE -s comphet_side -s denovo -p A1257-220114-VAR-Botto-Leukodystrophy.ped -o A1257-220114-VAR-Botto-Leukodystrophy_Final_1642265647.vcf.gz.slivar2.vcf.gz

and the output

> slivar version: 0.2.7 71af7d12881ae0590c6d2a97ef2b282cc93fe7c6
[slivar tsv] warning! didn't find ANN in header in A1257-220114-VAR-Botto-Leukodystrophy_Final_1642265647.vcf.gz.slivarch.vcf.gz trying other fields
[slivar tsv] warning! didn't find CSQ in header in A1257-220114-VAR-Botto-Leukodystrophy_Final_1642265647.vcf.gz.slivarch.vcf.gz trying other fields
[slivar tsv] warning! didn't find CSQ in header in A1257-220114-VAR-Botto-Leukodystrophy_Final_1642265647.vcf.gz.slivarch.vcf.gz trying other fields
SIGSEGV: Illegal storage access. (Attempt to read from nil?)

And here's the input VCF that was annotated with bcftools csq and vcfanno https://home.chpc.utah.edu/~u0691312/A1257-220114-VAR-Botto-Leukodystrophy_Final_1642265647.vcf.gz.slivarch.vcf.gz
And the ped file https://home.chpc.utah.edu/~u0691312/A1257-220114-VAR-Botto-Leukodystrophy.ped

Had the same error with multiple, now up to 3, VCFs. But works fine on a simple chr21 only test VCF

brentp · 2022-04-15T07:05:48Z

Hi Matt, thanks for the test-case. You have this INFO:

BCSQ=3_prime_utr|LGSN|ENST00000370658|protein_coding,3_prime_utr|LGSN|ENST00000622415|protein_coding,@63280473;REVEL=0.698;gnomad_popmax_af=6.54707e-05;gnomad_n_hets=2;gnomad_n_homalt=0;genic;highest_impact_order=29;comphet_side=UDN810123

at chr6:63280472 G/A. This is because you ran bcftools csq with -p. You should instead use -l. I'll have this give a message in the next release, but for now, you can re-run bcftools csq.

mvelinder · 2022-04-15T15:24:52Z

Worked perfectly with -l thanks as always @brentp !

brentp closed this as completed Apr 28, 2019

genomics-geek added a commit to chopdgd/bfx-tools-wdl that referenced this issue Sep 24, 2019

Added zgrep/grep functions

7e47b9c

This is needed to remove GATK.CommandLine from VCF header. slivar errors out when these are present. See: brentp/slivar#27 (comment)

genomics-geek mentioned this issue Sep 25, 2019

use RankSum's for filtering #36

Closed

genomics-geek added a commit to chopdgd/bfx-tools-wdl that referenced this issue Oct 11, 2019

Added zgrep/grep functions

6506486

This is needed to remove GATK.CommandLine from VCF header. slivar errors out when these are present. See: brentp/slivar#27 (comment)

seboyden mentioned this issue Apr 23, 2021

SIGSEGV: Illegal storage access. (Attempt to read from nil?) on make-gnotate #90

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brentp added a commit that referenced this issue Jun 28, 2021

fix long-standing bug (#27) that would cause sigsegv in some cases

d64b67c

brentp added a commit that referenced this issue Apr 15, 2022

add warning for bad CSQ (#27)

2b76e2c

SIGSEGV: Illegal storage access. (Attempt to read from nil?) #27

SIGSEGV: Illegal storage access. (Attempt to read from nil?) #27

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