{"action":"created","issue":{"url":"https://api.github.com/repos/jts/nanopolish/issues/182","repository_url":"https://api.github.com/repos/jts/nanopolish","labels_url":"https://api.github.com/repos/jts/nanopolish/issues/182/labels{/name}","comments_url":"https://api.github.com/repos/jts/nanopolish/issues/182/comments","events_url":"https://api.github.com/repos/jts/nanopolish/issues/182/events","html_url":"https://github.com/jts/nanopolish/issues/182","id":242202518,"number":182,"title":"nanopolish variants ","user":{"login":"yusmiatiliau","id":22285666,"avatar_url":"https://avatars0.githubusercontent.com/u/22285666?v=4","gravatar_id":"","url":"https://api.github.com/users/yusmiatiliau","html_url":"https://github.com/yusmiatiliau","followers_url":"https://api.github.com/users/yusmiatiliau/followers","following_url":"https://api.github.com/users/yusmiatiliau/following{/other_user}","gists_url":"https://api.github.com/users/yusmiatiliau/gists{/gist_id}","starred_url":"https://api.github.com/users/yusmiatiliau/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yusmiatiliau/subscriptions","organizations_url":"https://api.github.com/users/yusmiatiliau/orgs","repos_url":"https://api.github.com/users/yusmiatiliau/repos","events_url":"https://api.github.com/users/yusmiatiliau/events{/privacy}","received_events_url":"https://api.github.com/users/yusmiatiliau/received_events","type":"User","site_admin":false},"labels":[{"id":158430384,"url":"https://api.github.com/repos/jts/nanopolish/labels/enhancement","name":"enhancement","color":"84b6eb","default":true}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":10,"created_at":"2017-07-11T22:24:54Z","updated_at":"2018-02-16T02:38:58Z","closed_at":null,"author_association":"NONE","body":"Hi, \r\n\r\nI am using MinION to call multiple SNPs and in-dels from a multiplex PCR. in total, I have 15 amplicons. One of my reference samples have 2 SNPs and 1 one-base deletion (Heterozygotes). \r\n\r\n\"/media/WORKSPACE/cen/nanopolish/scripts/nanopolish_makerange.py\" 15amplicon_formated.fasta | parallel --results barcode022_nanopolish.results -P 8 nanopolish variants --consensus polished.{1}.fa -w {1} -r barcode02_nanopolish.fa -b barcode02_nanopolish.sorted.bam -g 15amplicon_formated.fasta -t 4 --min-candidate-frequency 0.1 \r\n\r\n\r\nI have several questions:\r\n1. in both of the SNPs called by nanopolish variants, it gave me two lines:\r\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tsample\r\nABCB1\t102\t.\tT\tC\t51976.9\tPASS\tTotalReads=3821;AlleleCount=1;SupportFraction=0.413547\tGT\t1\r\nABCB1\t102\t.\tT\tC\t51667.2\tPASS\tTotalReads=3824;AlleleCount=1;SupportFraction=0.969851\tGT\t1\r\n\r\n#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  sample\r\nVKORC1rs7294    115     .       G       A       7746.0  PASS    TotalReads=1595;AlleleCount=1;SupportFraction=0.792303  GT      1\r\nVKORC1rs7294    115     .       G       A       7718.2  PASS    TotalReads=1595;AlleleCount=1;SupportFraction=0.891691  GT      1\r\n\r\nwhat is the difference between those two lines? For ABCB1, the sample should have CC genotype, so I think the second line is correct. But, if I don't know the genotype, how can I tell which one should I use?\r\n\r\n2. I try to write the results into vcf file, using this command:\r\n\r\n\"/media/WORKSPACE/cen/nanopolish/scripts/nanopolish_makerange.py\" 15amplicon_formated.fasta | parallel --results barcode022_nanopolish.results -P 8 nanopolish variants --consensus polished.{1}.fa -w {1} -r barcode02_nanopolish.fa -b barcode02_nanopolish.sorted.bam -g 15amplicon_formated.fasta -t 4 --min-candidate-frequency 0.1 --o barcode022_nanopolish.vcf\r\n\r\nbut the vcf file only contained the ABCB1 variants, and don't the other one, what arguments should I add?\r\n\r\n2. the nanopolish variants failed to call the one-base deletion. when I looked at the bam file (IGV), the deletion site has 1213 read depth, and the deletion depth is 664, which is quite good. Do you have any idea, so the deletion would be called by nanopolish variants?\r\n\r\nThanks a bunch!\r\n\r\nCen\r\n"},"comment":{"url":"https://api.github.com/repos/jts/nanopolish/issues/comments/366129453","html_url":"https://github.com/jts/nanopolish/issues/182#issuecomment-366129453","issue_url":"https://api.github.com/repos/jts/nanopolish/issues/182","id":366129453,"user":{"login":"yusmiatiliau","id":22285666,"avatar_url":"https://avatars0.githubusercontent.com/u/22285666?v=4","gravatar_id":"","url":"https://api.github.com/users/yusmiatiliau","html_url":"https://github.com/yusmiatiliau","followers_url":"https://api.github.com/users/yusmiatiliau/followers","following_url":"https://api.github.com/users/yusmiatiliau/following{/other_user}","gists_url":"https://api.github.com/users/yusmiatiliau/gists{/gist_id}","starred_url":"https://api.github.com/users/yusmiatiliau/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yusmiatiliau/subscriptions","organizations_url":"https://api.github.com/users/yusmiatiliau/orgs","repos_url":"https://api.github.com/users/yusmiatiliau/repos","events_url":"https://api.github.com/users/yusmiatiliau/events{/privacy}","received_events_url":"https://api.github.com/users/yusmiatiliau/received_events","type":"User","site_admin":false},"created_at":"2018-02-16T02:38:58Z","updated_at":"2018-02-16T02:38:58Z","author_association":"NONE","body":"Thanks!"}}
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