qbasepileup
-This tool is dated due to some input file formats (dccq, dcc1) no longer being available!
Introduction
qbasepileup performs base pileup on positions of interest in a BAM
file and produces base coverage information and various others
metrics on the reads at the positions of interest.
Installation
qbasepileup requires java 21 and (ideally) a multi-core machine (5 threads are run concurrently) with at least 20GB of RAM.
- To do a build of qbasepileup, first clone the adamajava repository using "git clone":
git clone https://github.com/AdamaJava/adamajava
Then move into the adamajava folder:
cd adamajava
Run gradle to build qbasepileup and its dependent jar files:
./gradlew :qbasepileup:build
This creates the qbasepileup jar file along with dependent jars in the qbasepileup/build/flat folder
Usage
A general invocation of qbasepileup looks like:
java -jar qbasepileup.jar -m mode \
-i file.bam -r ref.fa -s positions.txt -o pileup.txt --log file.log
Options
Option Description
------ -----------
-V, -v, --version Print version info.
-b <txt file> Opt (coverage and snp mode), path to tab delimited file with list of bams.
--bq <Integer> Opt (snp related mode), minimum base quality score for accepting a read. Def = null.
--dup Opt (indel and snp mode), a flag to include duplicates reads.
-f [format] Opt(snp mode) snp file format: [dcc1, dccq, vcf, tab, maf].Def=dcc1. or
Opt(coverage mode), snp file format: [dcc1, dccq, vcf, tab, maf, gff3, gtf]. Def=dcc1.
--filter <query> Opt, a qbamfilter query to filter out BAM records. Def=null.
--gatk Opt (indel mode), a flag to conform gatk format, but do nothing.
-h, --help Shows this help message.
--hdf <hdf file> Opt (snp mode), path to hdf file which header contains a list of bams.
--hp <Integer> Opt (indel mode), base around indel to check for homopolymers. Def=10.
-i <bam file> Opt (coverage and snp mode), specify a single SAM/BAM file here.
--ig <dcc1> Req (indel mode), path to germline indel file in dcc1 format.
--in <bam file> Req (indel mode), path to normal bam file
--ind <y|n> Opt (snp related mode), include reads with indels [y,n]. Def=y.
--intron <y|n> Opt (snp related mode), include reads mapping across introns [y,n]. Def=y.
--is <dcc1> Req (indel mode), path to somatic indel file in dcc1 format.
--it <bam file> Req (indel mode), path to tumour bam file
--log Req, log file.
--loglevel Opt, logging level required, e.g. INFO, DEBUG. Default INFO.
-m <mode> Opt, Mode [snp, compoundsnp, snpcheck, indel, coverage]. Def=snp.
--mincov <Integer> Opt, report reads that are less than the mininmum coverage option.
--mq <Integer> Opt (snp related mode), minimum mapping quality score for accepting a read. Def = null.
-n <Integer> Opt (indel mode), bases around indel to check for other indels. Def=3.
--novelstarts <y|n> Opt (snp related mode), report novelstarts rather than read count [Y,N], Def=y.
-o <txt file> Req (coverage and snp related mode), the output file path.
--of <format> Opt (snp mode only), output file format [columns]. this option only works with input snp
file format is tab, otherwise it will ignored.
--og <dcc1> Req (indel mode), output file for germline indels.
--os <dcc1> Req (indel mode), output file for somatic indels.
-p [profile] Opt (snp mode), pileup profile type [torrent,RNA,DNA, standard]. Def="standard".
--pd <pindel_deletions> Req (indel mode), path to normal bam file
--pindel Opt (indel mode), a flag to conform pindel format, but do nothing.
-r <fasta file> Req (indel and snp mode), path to reference genome fasta file.
-s <txt file> Req (coverage and snp mode), path to tab delimited file containing snps.
--sc <Integer> Opt (indel mode), bases around indel to check for softclip. Def=13.
--strand <y|n> Opt (snp related mode), separate coverage by strand [y,n]. Def=y.
--strelka Opt (indel mode), a flag to conform strelka format, but do nothing.
-t [Integer] Opt, number of worker threads (yields n+2 total threads). Def=1.
Modes
coverage
Reads one or more BAM files, and a file containing reference ranges and piles up the reads around the indel to count the number of reads covering each position in the range.
snp
Reads one or more BAM files, a reference genome, and a file containing positions of SNPs. It finds the reference genome base at the SNP position as well as the bases found at that position in all reads aligned to that region. Coverage per nucleotide is reported and the total coverage at that position is reported. By default, duplicates and unmapped reads are excluded.
compoundsnp
-This mode is deprecated due to the input snp position file format (dcc1) is no longer available!
In this mode, qbasepileup reads one or more BAM files, a reference genome, and a file containing positions of compound SNPs (SNPs that sit next to each other). It finds the reference genome base at the compound SNP positions as well as the bases found at that position in all reads aligned to that region. Coverage per nucleotide is reported and the total coverage at that position is reported. By default, the filter is:
and( Flag_DuplicateRead==false, CIGAR_M>34, MD_mismatch <= 3, option_SM > 10)
For a more detailed description of qbamfilter and how it works to filter reads in and out of a particular analysis, seeqbamfilter.
This mode is for compound SNPs, is very similar to snp mode except:
- Only dcc1 format (
-f) is currently accepted - Default filter is:
and(Flag_DuplicateRead==false, CIGAR_M>34, MD_mismatch<=3, option_SM>10)
indel
-This mode is deprecated due to the indle file format (dcc1) is no longer available!
Reads tumour and normal BAM files, a reference genome, and somatic and/or germline files containing positions of indels and pileups the reads around the indel to count a number of metrics. Metrics include:
- total reads
- number of reads that span the indel
- number of reads with the indel
- number of novel starts with the indel
- number of reads with nearby soft clipping
- number of reads with nearby indels
Examples
- Somatic and Germline input files in pindel format
qbasepileup -t 2 -m indel -r reference.fa --pindel \
--it tumour.bam --in normal.bam \
--is somatic.input.dcc1 --ig germline.input.dcc1 \
--os somatic.output.dcc1 --og germline.output.dcc1 \
--log basepileup.log
- Somatic input file in gatk format
qbasepileup -t 2 -m indel --it tumour.bam --in normal.bam \
--is somatic.input.dcc1 --os somatic.output.dcc1
--log basepileup.log -r reference.fa --gatk
- Germline input file in pindel format
qbasepileup -t 2 -m indel --it tumour.bam --in normal.bam \
--ig germline.input.dcc1 --og germline.output.dcc1
--log basepileup.log -r reference.fa --pindel