pairdoc

Introduction In cancer genome sequencing studies, in order to infer a somatic mutation at a position, both tumor and its matched normal sample should have sufficient coverages at that position. Pairdoc is designed for calculating tumor-normal pair-matched depth of coverage in tumor sequencing studies. It is an efficient multi-threads C program to calculate various coverage statistics for exons, protein coding regions (CDS) and the whole genome using Binary Alignment/Map (BAM) files. Installation All C source codes of the program are packed in pairdoc-.tar.gz. It can be compiled under 32 or 64 bit Linux/Unix operation systems. First, uncompress it to one file folder on disk, then, use “make build64” or “make build32” to compile and generate the final executable binary program named pairdoc, respectively for 64 or 32 bit Linux/Unix operation systems. Detail Program:

pairdoc.0.1.0
faidx.h
razf.c
khash.h
bam2bcf.h
kaln.h
ksort.h
pairdoc-user-manual-v0.0.1.pdf
sam.c
bam.c
commfun.c
bam.h
errmod.h
bam_aux.c
Makefile
exoncov.c
knetfile.c
exoncov.h
bgzf.c
faidx.c
sam_header.c
kstring.c
kstring.h
kseq.h
razf.h
bam_maqcns.h
knetfile.h
bam_import.c
bam_endian.h
bam_pileup.c
sam.h
klist.h
glf.h
bam_index.c
commfun.h
sam_header.h
bgzf.h