(Un)expected (Mis)matches Tables

Theoretical Method

Expected Matches are extracted from the title file provided for the pipeline run. Any samples with the same Patient ID in the title file are expected to match. The Expected matches that were extracted from the title file are printed in the ExpectedMatches.txt file in the QC_Results/FPResults folder from the pipeline.

The pairs of samples are assigned their “Status” based on the following conditions:

• Expected Match: Expected to match from Title file and discordance rate<5% .

• Expected Mismatch: Not expected to match from Title file and discordance rate>=5%.

• Unexpected Match: Discordance rate<5% but not expected to match from Title file.

• Unexpected Mismatch: Discordance rate>=5% but Expected to match from Title file.

Additionally, UnexpectedMismatch.txt and UnexpectedMatch.txt are available in QC_Results/FPResults.

These calculations were done using All Unique (unfiltered) 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_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

  • Unexpected_Match.pdf

  • Unexpected_Mismatch.pdf

  • FPResults/UnexpectedMismatch.txt and FPResults/UnexpectedMatch.txt

  • Geno_compare.txt (All pair-wise genotyping comparison results for the samples in the run, along with their status)

Interpretations

Unexpected Matches and Mismatches are printed in Unexpected Matches and Unexpected Mismatches tables in the QC PDF. If there are no unexpected matched/mismatched, an empty table will be in the PDF.