To filter variants with a low minor allele frequency (MAF) from a variant call format (VCF) file, we can use softwares such as bcftools, plink or R. What is minor…
This week, we will see how to make all variants heterozygous in a VCF file. The purpose of this step is to use this file for an unbiased allele-specific read…
Today, we will see how to filter reads in a BAM file that overlap indels defined in a VCF file using the samtools software. Tools used In this post, we…
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