ekg/freebayes — Issue #24: Called variants with same base as reference sequence
Author: chapmanb
Created: 2011-12-14 01:56:44+00:00
State: open

Freebayes will ouput variant calls that have the same base as the reference sequence:

#CHROM POS ID REF ALT QUAL FILTER
5 165062085 . G G 82.086 .

These cause GATK variant manipulation tools to raise an error when working downstream with Freebayes calls, which identified the issue.

Here is a BAM file with 2 reads that reproduces the problem, using the Broad GRCh37 genome:

https://s3.amazonaws.com/chapmanb/freebayes_nochange_call.bam
ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/1.2/b37/human_g1k_v37.fasta.gz

freebayes -b freebayes_nochange_call.bam -v test_nochange.vcf -f GRCh37.fa

Please let me know if any other information would be helpful.