Input VCF files need to be in a certain format?

Integrative-Transcriptomics / MUSIAL

Summarize SNV and indel information on single gene or genome level together with other relevant statistics based on .vcf files.

https://tuevis.cs.uni-tuebingen.de/musial/

GNU General Public License v3.0

5 stars 1 forks source link

Input VCF files need to be in a certain format? #6

Open Kelzor opened 4 years ago

Kelzor commented 4 years ago

Hello!

Do the VCF files need to have been generated by UnifiedGenotyper/EAGER, or can MUSIAL interpret VCFs from freebayes or HaplotypeCaller?

Thanks, Kelly

alex-seitz commented 4 years ago

Hi Kelly, MUSIAL uses the htsjdk-library to parse the vcf-Files. If I remember correctly, it has problems with freebayes for some reason. Everything generated with GATK should be fine tough.

Best, Alex