huang-j / snv-calling

Runs on Mutect2/MuSE with some processing for SureCall

SNV-calling

Runs on Mutect2/MuSE with some processing for SureCall

Each caller has it's own annotationfilter file because of different structuring.

SureCall

agiprocv2.sh // Requires Agent from Agilent, bwa-mem, samtools

Inputs:

-d bottom directory

-l a list of samples to be processed

-b bed file

Outputs:

Trimmed/: trimmed fastq

Bams/: Barcode collapsed and unbarcode collapsed samples

SureCallAnnotationFilter.R

Inputs:

Annovar annotated vcf file off of SureCall (SNPPT)

Outputs:

filtered table

MuSE

rMuSE.sh // Requires MuSE, pretty much no other documentation other than those two lines

Has to be paired samples in form:

path/to/tumor path/to/normal samplename

runMuSE.py // For HPC jobs

MuTect2

rMutect2Chr.sh // Requires gatk/4.1.0.0+ (4.0 has weird issues with Mutect)

Runs Mutect. Note the usage() for required fields

runMutect2Chr.py // unpaired

runMutect2MatchChr.py // paired

Both generate Jobs for the HPC. To run chr by chr it's necessary to input a interval file of just that chr.

e.g. in bash:

for f in $(find {location of interval files} | grep 'chr') ; do

  python runMutect2MatchChr.py -f [tab separated paired file locations] -i $f

done

GatherVCF.py //also requires gatk/4.1.0.0+

combines the VCF files from chr to chr runs to one single VCF

note: only does chr1:22 (no M, X, Y)

gatkPoN.sh

create PoN from single sample Mutect2 runs