Picard CollectWGSMetrics vs QualiMap vs samtools stats

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Damian Fermin

• April 23, 2024 15:52

REQUIRED for all errors and issues:
a) GATK version used:  v4.3.0.0
b) Exact command used:

gatk CollectWgsMetrics --MAX_RECORDS_IN_RAM 10000000 -R $FASTA -I $BAM -O $OUT

I'm having trouble reconciling the output of GATK CollectWgsMetrics with the output I get from QualiMap and samtools stats for the same BAM file:

• QualiMap claims the mean coverage of the file is 30X
• CollectWgsMetrics claims the mean coverage of the file is 18.4X
• Samtools stats claims that the coverage is 30X

I'm not sure which output to believe nor why I'm getting such different output. 
Any suggestions?

Thanks,

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• 

  Gökalp Çelik

  • April 23, 2024 16:04

  Hi Damian Fermin

  These tools all use different thresholds to accept reads for calculation. 

  Picard CollectWgsMetrics uses the below parameters as default and therefore may end up reporting a lower coverage. You may set both parameters to 0 to compare your results with others. 

  --MINIMUM_BASE_QUALITY,-Q <Integer>
                                Minimum base quality for a base to contribute coverage. N bases will be treated as having
                                a base quality of negative infinity and will therefore be excluded from coverage
                                regardless of the value of this parameter.  Default value: 20. 
  
  --MINIMUM_MAPPING_QUALITY,-MQ <Integer>
                                Minimum mapping quality for a read to contribute coverage.  Default value: 20.

  There are also other parameters present such as COVERAGE_CAP and LOCUS_ACCUMULATION_CAP both of which may affect your output. 

  I hope this helps. 

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