Hi Alexey,
Yes, CalculateHsMetrics does not care about the strand column in the
interval list files. This file format is used in several places in the
Picard tools, and strand is only relevant for some of those uses.
-Alec
On 7/14/14, 2:55 PM, Alexey Larionov wrote:
Hello,
CalculateHsMetrics requires target and bait files in picard interval
list format. This file format requires information about the strand.
At present Illumina does not provide explicit strand information for
targets and probes for Nextera Rapid Exome kit. So I tried
CalculateHsMetrics with all features set to "+",or to "-" strand, or
random allocation of +/- strand to each feature. The results are
identical. Is it what is expected? How CalculateHsMetrics uses
strand information from targets and baits files?
Illumina says that their probes are designed against the coding
strand. Assuming the gene is mapped on "positive" strand. What
strand should I assign to the probe and to the target when I generate
the picard interval list file?
Thank you
Alexey
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