Question: How To Get Strand Information For List Of Intervals In .Bed File (To Use With Picard Calculatehsmetrics)
1
gravatar for User6891
7.0 years ago by
User6891280
Europe
User6891280 wrote:

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?

bed picard strand • 3.8k views
ADD COMMENTlink modified 7.0 years ago by brentp23k • written 7.0 years ago by User6891280
2
gravatar for brentp
7.0 years ago by
brentp23k
Salt Lake City, UT
brentp23k wrote:

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
ADD COMMENTlink written 7.0 years ago by brentp23k

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

ADD REPLYlink written 7.0 years ago by User6891280

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.

ADD REPLYlink written 7.0 years ago by Dan D7.1k
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