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Hapcounter

Minimal tool to count genotypic frequencies at two loci covered by same read fragments

Usage

Takes position sorted BAM file along with the two genomic loci, and outputs the base counts at each loci, and genotype frequencies of same fragments spanning the two loci

$./hapcounter
Usage: hapcounter <bam> <region1> <region2> [qc:ture/false]
       hapcounter molt4LMO2.bam chr11:33881016 chr11:33956761
       hapcounter molt4LMO2.bam chr11:33881016 chr11:33956761 true

QC = true refers to removal reads with:

* mapping quality < 30
* is_mate_unmapped = false
* is_secondary = false
* is_supplementary = false

Example

$./hapcounter molt4LMO2.bam chr11:33881015 chr11:33956761
Base counts at chr11:33881015-33881015
2794.0
A|T|G|C|INDELS
18(0.01)|2234(0.80)|140(0.05)|402(0.14)|0(0.00)
----------------------------
Base counts at chr11:33956761-33956761
534.0
A|T|G|C|INDELS
3(0.01)|1(0.00)|1(0.00)|237(0.44)|292(0.55)
----------------------------
Genotypes on fragments spanning chr11:33881015 and chr11:33956761 (Insert length 75746bp)
G/INDEL 15(0.05)
A/C     5(0.02)
G/C     2(0.01)
C/A     1(0.00)
C/T     1(0.00)
C/C     99(0.36)
C/INDEL 2(0.01)
T/INDEL 136(0.50)
T/G     1(0.00)
T/C     12(0.04)

50% of fragments with T at chr11:33881015 also contain an INDEL at chr11:33956761

Installation

Requires rust

$cargo install --git https://github.com/CompEpigen/hapcounter

Above command will install hapcounter binary under path (~./cargo/bin/).

caveat

Have not checked with Deletions.