How To Get Strand Information For List Of Intervals In .Bed File (To Use With Picard Calculatehsmetrics)
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7.6 years ago
User6891 ▴ 290

Hi everyone,

I want to use Picard's CalculateHsMetrics tool. To do this one needs a BAIT_INTERVAL & TARGET_INTERVAL file, which both need to contain 5 columns (chromosome, start, end, strand & name). I want to test this on whole exome data. The company has a .bed file with the target (Nextera Exome), but this file does not contain information about the strand. Since this is mandatory for Picard, I was wondering if someone knows how to get this information? Is Picard actually using this information to calculate the metrics?

strand bed picard • 4.0k views
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7.6 years ago
brentp 23k

I usually just use "+" for all of them when I dont care. For capture, my regions look like (for columns chrom, start, end, strand, name):

chr1    3534355 3534595 +       chr1:3534355-3534595
chr1    3593248 3593368 +       chr1:3593248-3593368
chr1    3611230 3611590 +       chr1:3611230-3611590
chr1    3670534 3671089 +       chr1:3670534-3671089
chr1    3671123 3671483 +       chr1:3671123-3671483
chr1    3671632 3672740 +       chr1:3671632-3672740
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That's what I was planning to do too, but I want to be sure that picard HsMetrics is not using this strand information for some calculations

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For most metrics it does not. The CalculateHSMetrics tool is great, but is also very finicky and gives strange error messages. I've run this tool a lot so post again if you run into any problems.

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