search

samtools / bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
http://samtools.github.io/bcftools/
Other
680 stars 240 forks source link

if samtools can useRNA-Seq to calculate the SNP expression in VCF files. #1248

Closed Trandamere closed 4 years ago

Trandamere commented 4 years ago

Hi： I want to know if samtools can use RNA-Seq to calculate the SNP expression in VCF files.

tseemann commented 4 years ago

What does "SNP expression" mean?

Trandamere commented 4 years ago

Hi Just like this: Allele-specific splitting of alignments between genomes with known SNP genotypes. I just want to know if samtools can calculate the number and type of bases at a SNP site

pd3 commented 4 years ago

If I understand the question correctly, you probably want to determine the number of reference vs alternate bases at a site. This can be done by adding the FORMAT/AD field during variant calling bcftools mpileup -a FORMAT/AD. See also http://samtools.github.io/bcftools/howtos/variant-calling.html