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Forum: SOLiD 09-09-2015, 01:56 AM
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Views: 6,468
Posted By Waqasuddin Khan
SNP at every chromosome position


I SOLiD sequencing data. After aligning with SHRiMP2, I used samtools mpileup for SNP calling:

samtools mpileup -C50 -gf hg38.fa -o var.raw.bcf input.bam

bcftools call -o var.raw.vcf -O...
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