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ngs-fzb / MTBseq_source

MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.
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mpileup to vcf #47

Closed acebollada closed 4 years ago

acebollada commented 4 years ago

Hi, I'm newbie at bioinformatic and I have one question.Do you recommend me some tool that is suitable to convert mpileup files that MTBseq generates to vcf files to visualize in IGV?? Or is it possible with MTBSeq generates the vcf files? Thank you in advance

aspitaleri commented 4 years ago

Hi I have used VarScan for this purpose: java -jar VarScan.v2.3.9.jar mpileup2snp file.mpileup --output-vcf 1 --min-var-freq 0.75 > file.varscan75.vcf

HTH

acebollada commented 4 years ago

Thank you I'll test it

cutpatel commented 4 years ago

Unfortunately MTBseq is not giving you a vcf, this should definetly be changed in the future. Please be aware that the suggested workaround is a different variant caller that may give you other variants than the MTBseq variant calling routine.