Sex Mismatch

Theoretical Method

Sex is inferred by looking at the average coverage for Tiling_SRY_Y:2655301 and Tiling_USP9Y_Y:14891501 probes in the All Unique bams (found from the intervals file in the Waltz output for Pool B). When the sum of the average coverage per interval (2 on Y) is greater that 50, the sample is classified as male. If the inferred sex does not match the reported sex, it is classified as a mismatch. Reported sex is from the title file.

These calculations were done using All Unique (unfiltered) bams.

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

  • GenderMisMatch.pdf (Probably should be labeled as SexMisMatch.pdf)

  • FPResults/MisMatchedGender.txt (Probably should be labeled as MisMatchedSex.txt)

Interpretations

Sex mismatches are an indication of a sample mixup. Low coverage, especially in the Y Chromosome may lead to a false positive.