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User-defined coverage in CollectHsMetrics [Picard]

Hello Biostars!

Can anyone tell me how to get user-defined coverage from Picard? Right now, I am using CollectHsMetrics to get coverage like 1x, 2x, 10x - 50x, 100x. But what if I want to get coverage at 5x ?

Please help me. Thank you in advance :)

Link to the tool : http://broadinstitute.github.io/picard/command-line-overview.html#Overview

next-gen picard coverage broadinstitute
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updated by sh001 • sh001 • written by anu014 anu014

Yes, I saw it now.. I am doing it.

Thanks Pierre.

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written by anu014 anu014

Hi, I'm bringing up an old post since I'm trying to obtain PCT target bases for 5x.

I'm not sure why we can't calculate it with the histogram values. What does the Histogram values represent?

The sum of all numbers in "high_quality_coverage_count" should be equal to "Total_reads" if we use Minimum_base_quality=0. Am I missing anything?

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written by sh001 • sh001

1 answer

You can't, it's hard-coded: https://github.com/broadinstitute/picard/blob/master/src/main/java/picard/analysis/directed/TargetMetricsCollector.java#L692

        metrics.PCT_TARGET_BASES_1X   = (double) targetBases[1] / (double) targetBases[0];
        metrics.PCT_TARGET_BASES_2X   = (double) targetBases[2] / (double) targetBases[0];
        metrics.PCT_TARGET_BASES_10X  = (double) targetBases[3] / (double) targetBases[0];
        metrics.PCT_TARGET_BASES_20X  = (double) targetBases[4] / (double) targetBases[0];
        metrics.PCT_TARGET_BASES_30X  = (double) targetBases[5] / (double) targetBases[0];
        metrics.PCT_TARGET_BASES_40X  = (double) targetBases[6] / (double) targetBases[0];
        metrics.PCT_TARGET_BASES_50X  = (double) targetBases[7] / (double) targetBases[0];
        metrics.PCT_TARGET_BASES_100X = (double) targetBases[8] / (double) targetBases[0];

alternatives:

  • change the code
  • use GATK DepthOfCoverage
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written by Pierre Lindenbaum Pierre Lindenbaum

Thank you for the reply.

I'll try DepthOfCoverage now. It seems better, I can use it even for WGS data too (without interval list).

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written by anu014 anu014

If this answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted. Upvote|Bookmark|Accept

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written by Pierre Lindenbaum Pierre Lindenbaum

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