WES -> recalibration matrix and Deduplication matrix reads number is very strange.
0
0
Entering edit mode
5 weeks ago
jk.kim • 0

Hello, everyone

I don't know this problem, recalibration matrix and Deduplication matrix read size.

At the first, I used the tools Gatk DeduplicationSpark and the step is dedup.bam -> recal.bam But, I will check the matrix so is very strange. Because dedup total read size example) 700,000 -> recal is example) 1,900,000 what happened to increase read size?

I think two problems. or more than the problem.

  1. original data experiments problem

or

  1. Gatk DeduplicationSpark optional is a problem ( check the opticalDuplicatePixelDistance ? or default size? )

====================================================== Example data)

  • Dedup.bam matrix
  • LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE Unknown Library 380347 72110005 327484 615657 257747 4243867 ...

    • recal.bam matrix
  • BAIT_SET BAIT_TERRITORY BAIT_DESIGN_EFFICIENCY ON_BAIT_BASES NEAR_BAIT_BASES OFF_BAIT_BASES PCT_SELECTED_BASES PCT_OFF_BAIT ON_BAIT_VS_SELECTED MEAN_BAIT_COVERAGE PCT_USABLE_BASES_ON_BAIT PCT_USABLE_BASES_ON_TARGET FOLD_ENRICHMENT HS_LIBRARY_SIZE HS_PENALTY_10 36632661 1 11542540300 4893421367 0 1 0 0.702273 315.088776 0.700896 0.403819 59.46704 471059915 ...

Best regards.

matrix recal dedup reads • 70 views
ADD COMMENT

Login before adding your answer.

Traffic: 1584 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6