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:
The VCF:
BBMap command:
I think BBMap could be a very powerful set of tools and I am expecting I am missing something pretty basic!
Code:
vcf-validator tmp.vcf Wrong number of fieldsin tmp.vcf; expected 15, got 16. The offending line was: [... the first line of variants]
Code:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT FORMAT FORMAT FORMAT FORMAT FORMAT FORMAT
Code:
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
Comment