bbmap callvariants.sh multisample vcf format, wrong number of fields

[Greg]

Trying to use BBMap callvariants on multiple samples. The resulting VCF does not have the sample names and yields an error with any vcf tools:

vcf-validator tmp.vcf 
Wrong number of fieldsin tmp.vcf; expected 15, got 16. The offending line was: [... the first line of variants]

The VCF:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  FORMAT  FORMAT  FORMAT  FORMAT  FORMAT  FORMAT

BBMap command:

callvariants.sh multisample=t list=SamList out=tmp.vcf ref=genome.fa 
#ive also tried using the output command, no change
callvariants.sh multisample=t list=SamList out=tmp.vcf ref=genome.fa vcf0=S1,S2,S3,S4,S5,S5
#As well as each sample using the "in" command
callvariants.sh multisample=t in=S1.sam,S2.sam,S3.sam,S4.sam,S5.sam,S6.sam out=tmp.vcf ref=genome.fa overwrite=t vcf0=AO,GG,OG,SF,TH,Tum

I think BBMap could be a very powerful set of tools and I am expecting I am missing something pretty basic!

[Brian Bushnell]

Hi Greg,

Sorry about that, there was a bug that slipped in around v37.87 with regards to multisample VCF names. It's fixed in v37.96 which I will release this week.

-Brian

[Greg]

Okay cool, thanks for the quick response!

[denisDDS]

Same error here: downloaded BBMap 2 weeks ago, finishing my snp calling pipeline today, same problem and discovering the patch went out 10 days ago...

Thx for the fix

[Brian Bushnell]

Oh, yep - it's fixed now, sorry for not mentioning that!

[denisDDS]

I have another problem: when using vcf0=, followed by files locations separated by comma, callvariants.sh create subdirectory instead of just creating files at specified location.