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qBasePileup Indel

Ollie Holmes

In this mode, qbasepileup is a Java tool that 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 and number of reads with nearby indels.

Options

Option order is arbitrary.

  • --help, -h Shows usage and help text
  • --version, -v Shows current version number.
  • --log Required. Path to log file.
  • --loglevel Optional. Logging level, e.g. INFO,DEBUG. Default INFO.
  • --mode Required. Specify "indel"
  • --it Required. Path to tumour bam file
  • --in Required. Path to normal bam file.
  • --r Required. Path to reference genome
  • --is Required unless --ig option is present. Path to somatic dcc1 input file.
  • --ig Required unless --is options is present. Path to germline dcc1 input file.
  • --os Required if --is option is present. Path to somatic dcc1 outut file.
  • --og Required if --ig option is present. Path to germline dcc1 output file.
  • --t Optional. Thread number. Total thread number = number supplied + 2. Default 1 (total threads 3).
  • --filter Optional. Qbamfilter query to use
  • --sc Optional. Window of reference bases either side of indel to look for soft clipping. Default 13
  • --hp Optional. Window of reference bases either side of indel to look for homopolymer. Default 10
  • --n Optional. Window of reference bases either side of indel to look for other indels. Default 3
  • --strelka Optional. Strelka file type
  • --pindel Optional. Pindel file type. Is default.
  • --gatk Optional. GATK file type.

Examples

Somatic and Germline input files

qbasepileup -t 2 -m indel --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 -r reference.fa --pindel
  • Pindel file
  • Default soft clip window (13)
  • Default nearby indel window (3)
  • default homopolymer length (10)

Somatic input file

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
  • GATK file
  • Default soft clip window (13)
  • Default nearby indel window (3)
  • default homopolymer length (10)

Germline input file

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
  • Pindel file
  • Default soft clip window (13)
  • Default nearby indel window (3)
  • default homopolymer length (10)