User: cetin.m

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Posts by cetin.m

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Samtools mpileup genotype likelihood no PL field when all individuals are 0/0
... I am calling SNPS using samtools with the command: >>samtools mpileup -g -uf /mnt/NAS/share/Ref/human/hg19_chr/Chr_all.fa -l 1000G_D10KApart2.bed -q 15 -Q 20 -b CEPHbam.list -o CEPH_1000G_10Kapart.bcf I have 5 individuals in CEPHbam.list I am giving a reference SNP list in the file 1000G_D ...
pl samtools mpileup written 5 weeks ago by cetin.m0 • updated 5 weeks ago by Santosh Anand4.0k
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Comment: C: Understanding a VCF - Genotype likelihoods and genotype call
... I know. I am just trying to understand how the genotype likelihood part works. Do you have a comment about that? Thanks. ...
written 4 months ago by cetin.m0
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Understanding a VCF - Genotype likelihoods and genotype call
... I calculated genotype likelihoods from a BAM file with the command: "samtools mpileup -g -f filename" and got the BCF file. Then I used "bcftools call -c -v filename" to get the VCF. In the VCF file, I see the following two: 1 589051 . G A 7.79993 . DP=1;SGB=-0.37988 ...
sequence next-gen sequencing written 4 months ago by cetin.m0

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