Closed ghost closed 8 years ago
@sehrrot Can you share a few examples? I've been tweaking the genotyping methods.
Here are commands for both versions and one line of VCFs. Thanks
WHAM-GRAPHENING:v1.7.0-199-g6106
cmd: ~/wham/bin/WHAM-GRAPHENING -m 30 -b ./wham_test/wham.merge.test.vcf -a /home/ec2-user/reference/b37/human_g1k_v37.fasta -e MT -f sample1.bam,sample2.sample3.bam,sample4.bam 2> ./err.wham.step2.test.txt > ./wham_11993/wham.final.test.vcf
VCF
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2 sample3 sample4
1 884042 WG:DUP:WG:DUP:6ae33f9a C
source=WHAM-GRAPHENING:v1.7.0-184-gd30f
cmd: ~/wham-v1.7.0/bin/WHAM-GRAPHENING -m 30 -b ./wham_test/wham.merge.test.vcf -a /home/ec2-user/reference/b37/human_g1k_v37.fasta -e MT -f sample1.bam,sample2.sample3.bam,sample4.bam 2> ./err.wham.step2.test.txt > ./wham_11993/wham.final.test.vcf
VCF
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2 sample3 sample4
1 884042 WG:DUP:0e97c65e,3beaa0b8,82b86378,89d508ed C
@sehrrot Thank you. I'm currently working on improving the genotyping. I'll keep this in mind.
Hi
I recently updated the wham-graphening for the version: v1.7.0-199-g6106. I ran the genotyping for merged VCF (three samples in one VCF) and genotyping was not done for some of predictions, like ./. others have 0/1 or 1/1.
The previous version v1.7.0-184-gd30f was okay for the same input.