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qBasePileup SNP

Ollie Holmes

In this mode, qbasepileup 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.

Options

  • ---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.
  • -i Optional: snp or indel. Default snp
  • -i Required if no -b option. Path to bam file.
  • -b Required if no -i option. Path to tab delimited file with list of bams. File should contain 3 columns: Integer identifier, Donor, Path to bam file.
  • -s Required. Path to containing snps. Formats: dcc1,maf, tab delimited txt (see format option), dccq, vcf
  • -r Required. Path to reference genome fasta file.
  • -o Required. Output file name.
  • -of Optional. Output file format: rows or columns (default rows). Results for the output file listing each bam by row or column

  • -f Optional. Format of SNPs file. Default dcc1. Current options:

    • dcc1
    • maf
    • dccq
    • vcf
    • tab
      The tab option is a tab delimited text file with 4 columns and no header. Columns are: id,chromosome,start position,end position

  • -p Optional. Run a pileup profile. Default is "standard". Current options are: standard, DNA, RNA, torrent. If additional options are provided, these settings will be updated to reflect the user provided option. All profiles will ignore unmapped reads and reads where the DuplicateRead flag is true.

Profile Mapping quality Base quality Strand Specific Include introns Include indels Novelstarts
standard any any y y y n
torrent 1 0 n y y n
RNA 10 7 n y y y
DNA 10 10 y n y n
  • --filter Optional. Qbamfilter query to use
  • --t Optional. Thread number. Total thread number = number supplied + 2. Default 1 (total threads 4).
  • --strand Optional. Separate coverage by strand. (y or n, default y).
  • --mq Optional. Minimum mapping quality score for accepting a read. Default is any mapping quality ie no filtering.
  • --bq Optional. Minimum base quality score for accepting a read. Default is any base qual ie no filtering.
  • --intron Optional. Include reads with indels. (y or n, default y).
  • --ind Optional. Include reads mapping across introns. (y or n, default y).
  • --novelstarts Report number of novel starts for each base type, rather than number of reads. (y or n, default n).

Examples

Defaults with bam file list

qbasepileup -b bam_list.txt -s snps.dcc1 -r reference.fa -o output.pileup.txt --log log_file.log
  • Default file format is dcc1
  • Standard profile:
    • Print strand specific info
    • Include any base or mapping quality
    • Include reads in introns
    • Include reads with indels

Defaults with single input bam file

qbasepileup -i input.bam -s snps.dcc1 -r reference.fa -o output.pileup.txt --log log_file.log
  • Default file format is dcc1
  • Standard profile:
    • Print strand specific info
    • Include any base or mapping quality
    • Include reads in introns
    • Include reads with indels

Use of qbmafilter query

qbasepileup -b bam_list.txt -s snps.dcc1 -r reference.fa -o output.pileup.txt --log log_file.log --filter "option_SM > 30"
  • Default file format is dcc1
  • Standard profile.
  • Qbamfilter query of option_SM > 30

SNP file format is maf

qbasepileup -b bam_list.txt -s snps.maf -r reference.fa -o output.pileup.txt --log log_file.log -f maf

Torrent profile

qbasepileup -b bam_list.txt -s snps.maf -r reference.fa -o output.pileup.txt --log log_file.log -f maf -p torrent
  • File format is maf
  • Torrent profile:
    • Do not print strand specific info
    • Min base quality: 0
    • Min mapping quality: 1
    • Include reads in introns
    • Include reads with indels

Run with user defined filtering options

qbasepileup -i input.bam -s snps.dcc1 -r reference.fa -o output.pileup.txt --log log_file.log \
--strand n --indel n --intron n -bq 5 -mq 10
  • No strand specific base coverage information
  • Do not include reads with indels
  • Do not include reads in introns
  • Read must have a minimum mapping quality of 10
  • Read must have a minimum base quality of 5.

Novel starts

qbasepileup -b bam_list.txt -s snps.dcc1 -r reference.fa -o output.pileup.txt --log log_file.log --novelstarts
  • File format is dcc1
  • Print strand specific info
  • Include any base or mapping quality
  • Include reads in introns
  • Include reads with indels
  • Count only novel starts

Related

Wiki: qBasePileup