Duplex Minor Contamination

Theoretical Method

Minor contamination from duplex bams for tumor sample (identified by the title file) is additionally checked. This analysis is done using the same fingerprint SNP in identified in the FP_configuration file although there is a 200x coverage threshold.

This 200x coverage threshold essential limits the analysis to the 31 specfically designed FP_SNPs.

The Minor Contamination Rate is the average (mean) minor allele frequency from homozygous fingerprint SNPs, where homozygous sites as those harboring < 5% minor allele frequency in the sequence data.

These calculations were done using duplex bams. Allele counts are measured from waltz pileups from Pool A and B

Technical Methods

• Tool Used:

  • Waltz PileupMetrics

  • fingerprinting.py

• Input

  • output_dir : Directory to write the Output files to

  • waltz_dir_A: Directory with waltz pileup files for target set A

  • waltz_dir_B: Directory with waltz pileup files for target set B

  • waltz_dir_A_duplex: Directory with waltz pileup files for Duplex target set A

  • waltz_dir_B_duplex: Directory with waltz pileup files for Duplex target set B

  • fp_config: File with information about the SNPs for analysis (MSK-ACCESS-v1_0-TilingaAndFpSNPs.txt)

  • title_file: Title File for the run

• Output

  • FPResults/minorDuplex Contamination.txt

  • MinorDuplexContaminationRate.pdf

Interpretations

Samples with Duplex Minor contamination rates of >0.002 are considered contamination.