Tool: het pulldown from callstats

Call normal het sites and get their tumor coverage from a MuTect callstats file.

Normal het sites are called using the posterior odds ratio in a coverage-independent manner. The het site allele fraction is assumed to be beta distributed with a flat prior (1, 1):

af ~ beta(n_alt + 1, n_ref + 1)

A site is considered heterozygous if

abs(log(P[af ≥ 0.5] / P[af ≤ 0.5])) < 2.5

The threshold can be changed using --log_pod_threshold.

Normal het sites can also be called using a simple beta distribution test. To use this method, specify --use_beta_density. A site is considered heterozygous if

Prob[0.4 < af < 0.6] > 0.7

The interval bounds (0.4, 0.6) and probability cutoff (0.7) can be overridden.

Usage:

usage: hetpull.py [-h] -c callstats_in -r ref_in -o output_prefix 
                  [-s snplist_in] [-g] 
                  [--use_pod_genotyper] [--log_pod_threshold threshold] [--pod_min_depth depth]
                  [--use_beta_density] [--af_lb lowerbound] [--af_ub upperbound] [--dens cutoff]
                  [--max_frac_mapq0 mapq0_frac] [--max_frac_prefiltered prefiltered_frac]

Required arguments

• -c callstats_in: Path to MuTect 1 callstats file
• -r ref_in: Path to reference FASTA (directory must also contain FASTA index)
• -o output_prefix: Prefix of tumor/normal het site coverage. Tumor coverage will be output to <prefix>.tumor.tsv, normal coverage to <prefix>.normal.tsv.

Optional arguments

• -s snplist_in: Path to SNP site list, for output of only specific SNP sites. Should be formatted GATK-style, i.e.

  <chr>    <pos>    <pos>    <strand>    <alt>/<ref>
  

  Note that the second <pos> and <strand> can be arbitrary values; all that matters is the number of columns. This is to ensure compatibility with GATK's GetHetCoverage tool.

• -g: Output genotype file (default FALSE)

• --use_pod_genotyper: Use posterior odds method for genotyping (default)

• --log_pod_threshold threshold: Exclude positions above Log Posterior Odds threshold (default 2.5)

• --pod_min_depth depth: Exclude positions with read depth less than threshold, when using pod genotyper (default 10)

• --use_beta_density: Use beta distribution density test for genotyping

• --af_lb lowerbound: Lower bound on beta distribution interval (default 0.4)

• --af_ub upperbound: Upper bound on beta distribution interval (default 0.6)

• --dens cutoff: Probability cutoff (default 0.7)

• --max_frac_mapq0 mapq0_frac: Exclude all positions with more than this percentage of MAPQ0 alignments (default 0.05)

• --max_frac_prefiltered prefiltered_frac: Exclude all positions with more than this fraction of total reads prefiltered by MuTect (default 0.1)