{"action":"created","issue":{"url":"https://api.github.com/repos/samtools/samtools/issues/1064","repository_url":"https://api.github.com/repos/samtools/samtools","labels_url":"https://api.github.com/repos/samtools/samtools/issues/1064/labels{/name}","comments_url":"https://api.github.com/repos/samtools/samtools/issues/1064/comments","events_url":"https://api.github.com/repos/samtools/samtools/issues/1064/events","html_url":"https://github.com/samtools/samtools/issues/1064","id":454247648,"node_id":"MDU6SXNzdWU0NTQyNDc2NDg=","number":1064,"title":"Samtools to output RX tags for Unique Molecular Indexes (UMI)","user":{"login":"apallav","id":7781467,"node_id":"MDQ6VXNlcjc3ODE0Njc=","avatar_url":"https://avatars1.githubusercontent.com/u/7781467?v=4","gravatar_id":"","url":"https://api.github.com/users/apallav","html_url":"https://github.com/apallav","followers_url":"https://api.github.com/users/apallav/followers","following_url":"https://api.github.com/users/apallav/following{/other_user}","gists_url":"https://api.github.com/users/apallav/gists{/gist_id}","starred_url":"https://api.github.com/users/apallav/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/apallav/subscriptions","organizations_url":"https://api.github.com/users/apallav/orgs","repos_url":"https://api.github.com/users/apallav/repos","events_url":"https://api.github.com/users/apallav/events{/privacy}","received_events_url":"https://api.github.com/users/apallav/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2019-06-10T16:10:03Z","updated_at":"2019-06-11T13:23:40Z","closed_at":null,"author_association":"NONE","body":"Hi,\r\n\r\nI would like to know if there is a way in samtools algo to recognize and output UMI / uniq molecular index tags from bam files. ex:RX:Z tags. \r\n\r\nCould this be added as feature request if none is available currently?\r\n\r\nThanks,\r\n\r\nAparna"},"comment":{"url":"https://api.github.com/repos/samtools/samtools/issues/comments/500838855","html_url":"https://github.com/samtools/samtools/issues/1064#issuecomment-500838855","issue_url":"https://api.github.com/repos/samtools/samtools/issues/1064","id":500838855,"node_id":"MDEyOklzc3VlQ29tbWVudDUwMDgzODg1NQ==","user":{"login":"apallav","id":7781467,"node_id":"MDQ6VXNlcjc3ODE0Njc=","avatar_url":"https://avatars1.githubusercontent.com/u/7781467?v=4","gravatar_id":"","url":"https://api.github.com/users/apallav","html_url":"https://github.com/apallav","followers_url":"https://api.github.com/users/apallav/followers","following_url":"https://api.github.com/users/apallav/following{/other_user}","gists_url":"https://api.github.com/users/apallav/gists{/gist_id}","starred_url":"https://api.github.com/users/apallav/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/apallav/subscriptions","organizations_url":"https://api.github.com/users/apallav/orgs","repos_url":"https://api.github.com/users/apallav/repos","events_url":"https://api.github.com/users/apallav/events{/privacy}","received_events_url":"https://api.github.com/users/apallav/received_events","type":"User","site_admin":false},"created_at":"2019-06-11T13:23:40Z","updated_at":"2019-06-11T13:23:40Z","author_association":"NONE","body":"> By default, `samtools view` outputs all tags attached to a read, starting from column 12.\r\n> \r\n> There is a merged but unreleased pull request (#1001) that filters the reads based on tags, including **RX**. However, the filter only works with a supplied tag value, e.g.\r\n> `samtools view -d RX:AGTCGATA alignment.bam`\r\n> \r\n> But it's not very clear that this feature is what you are after. If you just want to list all the values of a tag present in a file, you can go with a grep filter:\r\n> `samtools view alignment.bam | grep -oE \"RX:Z:[acgtnACGTN-]+ | sort -u\"`\r\n\r\nI am sorry for not being clear. I would like to see if it is possible for samtools mpileup to give out tag information  just like it gives out Fastq header tags. \r\n\r\nI could use samtools view alignment.bam | grep -oE \"RX:Z:[acgtnACGTN-]+ | sort -u\" to pipe in to samtools mpileup but that info is lost in the mpile up non vcf or vcf output formats. \r\n\r\nI specifically work with non-vcf formats from samtools / mpileup.\r\n\r\nThanks for your help,\r\n\r\n-A"}}
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