{"action":"closed","issue":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/1537","repository_url":"https://api.github.com/repos/broadinstitute/gatk","labels_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1537/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1537/comments","events_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1537/events","html_url":"https://github.com/broadinstitute/gatk/issues/1537","id":137613266,"number":1537,"title":"[Bug] When pulling INDELs only, SelectVariants omits indels from MIXED sites","user":{"login":"sooheelee","id":11543866,"avatar_url":"https://avatars.githubusercontent.com/u/11543866?v=3","gravatar_id":"","url":"https://api.github.com/users/sooheelee","html_url":"https://github.com/sooheelee","followers_url":"https://api.github.com/users/sooheelee/followers","following_url":"https://api.github.com/users/sooheelee/following{/other_user}","gists_url":"https://api.github.com/users/sooheelee/gists{/gist_id}","starred_url":"https://api.github.com/users/sooheelee/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sooheelee/subscriptions","organizations_url":"https://api.github.com/users/sooheelee/orgs","repos_url":"https://api.github.com/users/sooheelee/repos","events_url":"https://api.github.com/users/sooheelee/events{/privacy}","received_events_url":"https://api.github.com/users/sooheelee/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-03-01T16:00:27Z","updated_at":"2016-03-01T16:04:09Z","closed_at":"2016-03-01T16:04:09Z","body":"This bug was posted for [gsa-unstable](https://github.com/broadinstitute/gsa-unstable/issues/1302) also, and is being posted here again at David R's request. \r\n\r\nIn my opinion, this bug is a high priority. Also, it impedes me in my documentation work. So if there is a workaround that I can use in the meanwhile, please share with me so I can continue writing my tutorial for indel realignment.\r\n\r\n#### How I found the bug\r\nI loaded both the input and output VCFs into IGV and compared the variants in each. Using IGV's tooltip feature and hovering over each variant, I can see the variant type.\r\n\r\n#### Bug description\r\nIt appears for those sites I checked, MIXED site INDELs are missing from the VCF with INDELs only. I created the INDELs only VCF using `SelectVariants` and `-selectType INDEL`. \r\n\r\n#### Command to recapitulate what I did\r\nHere is the command I used, where $GATK refers to `../GATK/private_unstable_builds/GenomeAnalysisTK_latest_unstable.jar`:\r\n\r\n    java -jar $GATK -R $BUNDLE_B37 -T SelectVariants -V chr10_1Mb_b37_dbsnp_138.vcf -o INDEL_chr10_1Mb_b37_dbsnp_138.vcf -selectType INDEL\r\n\r\nThe input file, `/humgen/gsa-hpprojects/GATK/tutorial/solexa/indel_realignment/population_snippet/chr10_1Mb_b37_dbsnp_138.vcf` is subset for variants in the interval 10:96000000-97000000. Let me know if you want my output file. I won't provide it since I assume this bug will be recapitulated with the input and command above.\r\n\r\n"}}