qbasepileup indel mode

java -jar qbasepileup.jar -m indel ...

In this mode, qbasepileup reads tumour and normal BAM files, a reference genome, and somatic and/or germline files containing positions of indels. It creates pileups of 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.

Options

Option order is arbitrary.

--help      Show help message.
--version   Show version.

--log       Required. Path to log file.
--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.

--loglevel  Optional. Logging level, e.g. INFO,DEBUG. Default INFO.
--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 -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
  • 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)