Entering edit mode
5.6 years ago
evelyn
▴
230
I am using bcftools
to make vcf
from sorted bam
using:
bcftools mpileup -Ov -f ref.fa sorted.bam | bcftools call -mv -o sample.vcf
But I want to make a single vcf
from multiple sorted bam
files using bcftools
with SNPs from each sorted bam
. Thanks!
Thanks! But I am looking for making a
vcf
file for multiplesorted bam
files where thevcf
hasALT
bases like this:You could try making the VCFs separately and then using GATK tools: https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_GenotypeGVCFs.php https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_CombineGVCFs.php
Is there any way to do the same with
vcftools
!