Filter reference segments from CNV caller output

[Jakob37]

Description of the bug

The CNV caller output segments contains, in addition to calls of duplications / deletions, the segments in between those. For these the allele is set to "0/0" and not marked deletion <DEL> or duplication <DUP> in the ALT column.

I suspect this to be an error - we don't want to continue processing the ranges between the actual call ranges. They should probably be filtered out before being merged with the outputs of the other SV-callers.

An example output is seen below. In short - my guess is that we want to remove all where the ALT column is . rather than <DEL> or <DUP>.

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  giab_sample
chr1    792501  CNV_chr1_792501_1632500 N       .       3076.53 .       END=1632500     GT:CN:NP:QA:QS:QSE:QSS  0/0:2:825:9:3077:12:123
chr1    1632501 CNV_chr1_1632501_1635500        N       <DEL>   29.40   .       END=1635500     GT:CN:NP:QA:QS:QSE:QSS  0/1:1:3:11:29:16:12
chr1    1635501 CNV_chr1_1635501_1709500        N       .       1829.22 .       END=1709500     GT:CN:NP:QA:QS:QSE:QSS  0/0:2:72:4:1829:3:16
chr1    1710501 CNV_chr1_1710501_1712500        N       <DEL>   18.93   .       END=1712500     GT:CN:NP:QA:QS:QSE:QSS  0/1:1:2:9:19:37:3
chr1    1712501 CNV_chr1_1712501_1714500        N       <DEL>   422.43  .       END=1714500     GT:CN:NP:QA:QS:QSE:QSS  1/1:0:2:221:422:239:185
chr1    1714501 CNV_chr1_1714501_2121500        N       .       3076.53 .       END=2121500     GT:CN:NP:QA:QS:QSE:QSS  0/0:2:402:2:3077:26:34
chr1    2121501 CNV_chr1_2121501_2124500        N       <DEL>   27.26   .       END=2124500     GT:CN:NP:QA:QS:QSE:QSS  0/1:1:3:21:27:22:26
chr1    2124501 CNV_chr1_2124501_2651500        N       .       3076.53 .       END=2651500     GT:CN:NP:QA:QS:QSE:QSS  0/0:2:514:63:3077:53:22
chr1    2656501 CNV_chr1_2656501_2672500        N       <DEL>   94.12   .       END=2672500     GT:CN:NP:QA:QS:QSE:QSS  0/1:1:4:19:94:18:53
chr1    2674501 CNV_chr1_2674501_2675500        N       <DUP>   2.49    .       END=2675500     GT:CN:NP:QA:QS:QSE:QSS  ./.:3:1:2:2:2:2
chr1    2677501 CNV_chr1_2677501_2683500        N       .       32.24   .       END=2683500     GT:CN:NP:QA:QS:QSE:QSS  0/0:2:3:10:32:18:8

Command used and terminal output

No response

Relevant files

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System information

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[jemten]

yeah this looks wrong. I'll look into it

[jemten]

Is this from the gatk or cnvnator?

[Jakob37]

This is from GATK

[Jakob37]

I can try putting together a PR for this issue and the other remaining GATK issues (#442 and #444), if not someone else already is looking into it!

[jemten]

Sounds great @Jakob37 ❤️
@ramprasadn might be working on #442, so perhaps start on #444 until we can confirm with him