Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Keep "species" info from BAM to VCF

timflutretimflutre Montpellier, FranceMember

Hello,
I am using HaplotypeCaller (GATK v3.5) with an input BAM file which has a header line like this (just a fake example):

@SQ SN:chr1 LN:100000 SP:Arabis thal AS:2 M5:8668a646eada2f4 UR:file:refgenome_Atha_v2.fa

But the output VCF only has a subset of this information:

##contig=<ID=chr1,length=100000>
##reference=file:///home/me/tmp/refgenome_Atha_v2.fa

Is there a way to obtain something like this instead? (i.e. also indicate species, assembly and MD5 sum)

##contig=<ID=chr1,length=100000,assembly=2,md5=8668a646eada2f4,species="Arabis thal">

The information in the BAM file initially comes from a "dict" file generated by Picard CreateSequenceDictionary. So I tried to feed this "dict" file with the VCF file to Picard UpdateVcfSequenceDictionary, but it didn't give me species nor mD5 sum:

##contig=<ID=chr1,length=100000,assembly=2>

Thank you in advance,
Tim

Answers

Sign In or Register to comment.