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gvcf2vcf not filling in REF allele correctly #243

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mcshane opened this issue Apr 22, 2015 · 4 comments · Fixed by #244
Closed

gvcf2vcf not filling in REF allele correctly #243

mcshane opened this issue Apr 22, 2015 · 4 comments · Fixed by #244

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@mcshane
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mcshane commented Apr 22, 2015

When fixing #242 noticed that gvcf2vcf is just copying the REF allele from the beginning of the block. Command needs to take a reference fasta as input to fill in REF correctly.
@jmarshall
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Nice catch.

There is a -f/--fasta-ref option that fills in args.ref_fname and args.ref for convert --tsv2vcf. So that can be reused for --gvcf2vcf (and possibly some of the code refactored and moved to destroy_data() etc).

mcshane added a commit to mcshane/bcftools that referenced this issue Apr 22, 2015
@mcshane
gvcf fill ref allele from fasta
b49e93b 
* when filling in gvcf reference blocks need the
  samtools faidx indexed reference fasta to fill in
  the REF allele for each POS. reuse the `--fasta-ref`
  option already used by `--tsv2vcf`
* updated the test and test files to use the new option
* add new option to the man page

Fixes samtools#243
mcshane added a commit to mcshane/bcftools that referenced this issue Apr 22, 2015
@mcshane
gvcf fill ref allele from fasta
77a2697 
* when filling in gvcf reference blocks need the
  samtools faidx indexed reference fasta to fill in
  the REF allele for each POS. reuse the `--fasta-ref`
  option already used by `--tsv2vcf`
* updated the test and test files to use the new option
* add new option to the man page

Fixes samtools#243
mcshane added a commit to mcshane/bcftools that referenced this issue Apr 22, 2015
@mcshane
gvcf fill ref allele from fasta
cd1ebd1 
* when filling in gvcf reference blocks need the
  samtools faidx indexed reference fasta to fill in
  the REF allele for each POS. reuse the `--fasta-ref`
  option already used by `--tsv2vcf`
* updated the test and test files to use the new option
* add new option to the man page

Fixes samtools#243
@mcshane mcshane mentioned this issue Apr 22, 2015
Merged
@ryhui
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ryhui commented Dec 4, 2018 •
edited
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Hello, I just found out that this is fixed with uncompressed and compressed vcf output. If I use -Ou or -Ob, the REF allele is still copied from the beginning of the block.

@gtbil
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gtbil commented Nov 19, 2024

The issue ryhui indicated is still a problem. The workaround is to write to VCF rather than BCF.

pd3 added a commit that referenced this issue Dec 3, 2024
@pd3
Fix BCF output
d98d58f 
The command `convert --gvcf2vcf` was not filling the REF allele when BCF was output
because VCF API was not used, the alleles were rewritten directly. That works for
VCF, but not BCF output.

Fixes #243, finally
@pd3
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pd3 commented Dec 3, 2024

The BCF output is now fixed, finally. Thanks for reporting the bug, better to open a new issue next time, commenting on closed issues gets easily overlooked.

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gvcf fill ref allele from fasta mcshane/bcftools
5 participants
@jmarshall @pd3 @mcshane @ryhui @gtbil