We have decided to continue providing and supporting DepthOfCoverage and DiagnoseTargets for the foreseeable future. Going forward, we'll try to integrate them and develop their features to address the main needs of the community. To this end we welcome your continuing feedback, so please feel free to contribute comments and ideas in this thread.
To all who took the time to tell us what you find useful about DoC and DT (and what you wish it could do), a big thank you! This is always very useful to us because it helps us identify which features are most valuable to our users.
GATK 2.8 was released on December 6, 2013. Highlights are listed below. Read the detailed version history overview here: http://www.broadinstitute.org/gatk/guide/version-history
Note that this release is relatively smaller than previous ones. We are working hard on some new tools and frameworks that we are hoping to make available to everyone for our next release.
Now that DepthOfCoverage is being retired in GATK 2.4, I decided to investigate DiagnoseTargets. I have some questions.
1) Are there plans to support output formats other than VCF? What was great about DOC is I could easily send the output to anyone and it could be easily read. With DT, that requires additional processing.
2) DOC provided summary for intervals as well as samples. DT only does intervals. Is there a way to get per-sample info?
3) DOC output full intervals. DT only outputs the start positions. To get the end positions, an additional step is required. Can that be adjusted?
4) DOC provided coverage info for all intervals. DT only shows covered intervals, so if an interval is not covered, it will not be listed in the output. Is there a way to output all intervals?
Sorry if I sound too critical. I am a big fan of DepthOfCoverage and am disappointed to see it go.
Is DiagnoseTargets counting only reads that have mapped uniquely? Is that one of the default filters?
From the vcf I see that IDP - Average depth across the interval. Sum of the depth in a loci divided by interval size. LL - Number of loci for this sample, in this interval with low coverage (below the minimum coverage) but not zero ZL - Number of loci for this sample, in this interval with zero coverage.
I'm interested in the total number of reads mapped to each interval.
Is this true that IDP = #reads_in_this_interval/(LL+ZL) ? so if I want to extract #reads_in_this_interval, I can look at IDP*(LL+ZL)? I have different number of reads in each sample, so I first need to normalize it.
Is there a way to run DiagnoseTargets with a list of bam files, instead of multiple "-I bam_file" tags?
I a m running DiagnoseTargets on a list of intervals corresponding to targeted exons. In the result file, intervals are filtered by i.e. PASS, LOW_COVERAGE, COVERAGE_GAPS or NO_READS for each sample as well as for the sample set as a whole. In the individual-sample FORMAT fields, information on TF (filter) and IDP (average sample depth across interval) are given. How come I often see a combination like this?
Filtered as NO_READS, yet average depth of 96.09 across the interval? Of course, PART of the interval may be without reads, even more than the threshold set by --coverage_status_threshold, but this is what I understand is meant by COVERAGE_GAPS. I also wondered whether the reads might all have been totally filtered out due to low quality parameters and adjusted --minimum_base_quality and --minimum_mapping_quality to 0, but NO_READS are still flagged for a number of intervals, despite IDP being far from 0. Is this a bug, or have I misunderstood something?
is there an automatic way to generate an interval list for every 1kb in the reference sequence? I want to run DiagnoseTargets for every 1kb in the data.