The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Get notifications!

You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

Got a problem?

1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

Did we ask for a bug report?

Then follow instructions in Article#1894.

Formatting tip!

Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block as demonstrated here.

Jump to another community
Picard 2.10.4 has MAJOR CHANGES that impact throughput of pipelines. Default compression is now 1 instead of 5, and Picard now handles compressed data with the Intel Deflator/Inflator instead of JDK.
GATK version 4.beta.2 (i.e. the second beta release) is out. See the GATK4 BETA page for download and details.


ProtaeusProtaeus Member
edited September 2012 in Ask the GATK team


I previously reported an issue in which I could not emit all sites or all confident sites when using a ploidy of 1. I downloaded the most recent version and it seems to be able to print the reference calls in these modes. The odd thing is that the quality for all those calls is the same and really low, which I know isn't a reflection of reality in all cases given the knowledge we have about the sequence data and its relationship to the reference. It is also consistent across many samples, whether I run multiple samples through a single GATK run or a single sample on its own. I pasted in an example from a recent run (multiple samples in same run). The problem is that all of these reference calls get a LowQual filter, which makes it difficult to differentiate from good LowQual calls. Any thoughts as to if this is to be expected and why that might be?

Reference   72  .   T   .   3   LowQual DP=281;MQ=50.69;MQ0=0;NDA=1 GT  .   .   .   .   .   .
Reference   187 .   T   .   3   LowQual DP=301;MQ=51.00;MQ0=0;NDA=1 GT  .   .   .   .   .   .
Reference   188 .   C   .   3   LowQual DP=296;MQ=50.84;MQ0=0;NDA=1 GT  .   .   .   .   .   .
Reference   206 .   A   .   3   LowQual DP=292;MQ=50.14;MQ0=0;NDA=1 GT  .   .   .   .   .   .
Reference   1844    .   T   .   3   LowQual DP=369;MQ=58.59;MQ0=0;NDA=1 GT  .   .   .   .   .   .
Reference   1854    .   C   .   3   LowQual DP=363;MQ=58.63;MQ0=0;NDA=1 GT  .   .   .   .   .   .
Reference   1972    .   A   .   3   LowQual DP=345;MQ=59.11;MQ0=0;NDA=1 GT  .   .   .   .   .   .
Reference   1993    .   T   .   3   LowQual DP=355;MQ=58.54;MQ0=0;NDA=1 GT  .   .   .   .   .   .
Reference   2096    .   C   .   3   LowQual DP=355;MQ=58.92;MQ0=0;NDA=1 GT  .   .   .   .   .   .
Reference   2376    .   T   C   1105.23 .   AC=1;AF=0.167;AN=6;BaseQRankSum=-10.910;DP=417;Dels=0.00;FS=27.994;HaplotypeScore=1.6883;MLEAC=1;MLEAF=0.167;MQ=58.90;MQ0=0;MQRankSum=0.195;NDA=1;QD=16.75;ReadPosRankSum=-5.021;SB=-4.370e+02;Samples=Ba-4599_4    GT:AD:DP:GQ:MLPSAC:MLPSAF:PL    0:43,0:43:99:0:0.00:0,1813  1:0,66:66:99:1:1.00:1143,0  0:38,0:38:99:0:0.00:0,1627  0:127,0:127:99:0:0.00:0,5248    0:42,0:42:99:0:0.00:0,1739  0:100,0:100:99:0:0.00:0,4166


Post edited by Geraldine_VdAuwera on


  • You can disregard this question. I didn't realize this was indeed the same problem as my previous inquiry but hadn't tried emitting all sites, rather just confident sites. It sounds like this issue will be resolved with the new version, so I will hang tight until then.


Sign In or Register to comment.