Giters

aquaskyline / Clairvoyante

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

Geek Repo:Geek Repo

Github PK Tool:Github PK Tool

PASS flag for SNP and VCF header

fritzsedlazeck opened this issue · comments

commented

For certain applications it would be helpful to provide a PASS flag for trustworthy SNPs.

Also please consider to extend the VCF header with e.g. chromosome names and length.
Thanks
Fritz

commented

No problem. Will add a function for adding the PASS flag and headers.

commented

add contig tags in header; add PASS and LowQual filter tag if --qual is set for callVarBamParallel.py or callVarBam.py