Cross contamination

  • ID: cross_contamination_rate
  • Description: Estimation of inter-sample contamination rate of short paired-end sequencing high quality, non duplicated reads, primary alignments, mapped on GRCh38 assembly. No minimum mapping quality is imposed. It is critical that the (BAM/CRAM) alignment files be readily marked for duplicated reads and clipped bases.
  • Implementation details: In the NPM-sample-QC reference implementation, the estimation of inter-sample DNA contamination of short paired-end sequencing high quality, aligned sequence reads (BAM/CRAM) mapped on GRCh38 assembly with pre-calculated reference panel of 1000 Genome Project dataset from the VerifyBamID resource using VerifyBamID2 with NumPC “4” (# of Principal Components used in estimation), the key information “FREEMIX” in “.selfSM” in the results indicates the estimated contamination level.
  • Type: Float 4 decimal precision (eg. 0.0007)
  • Functionally equivalent implementations: