{"action":"created","issue":{"url":"https://api.github.com/repos/samtools/samtools/issues/880","repository_url":"https://api.github.com/repos/samtools/samtools","labels_url":"https://api.github.com/repos/samtools/samtools/issues/880/labels{/name}","comments_url":"https://api.github.com/repos/samtools/samtools/issues/880/comments","events_url":"https://api.github.com/repos/samtools/samtools/issues/880/events","html_url":"https://github.com/samtools/samtools/issues/880","id":335569124,"node_id":"MDU6SXNzdWUzMzU1NjkxMjQ=","number":880,"title":"samtools mpileup mis-reporting read depths","user":{"login":"drdna","id":3230221,"node_id":"MDQ6VXNlcjMyMzAyMjE=","avatar_url":"https://avatars0.githubusercontent.com/u/3230221?v=4","gravatar_id":"","url":"https://api.github.com/users/drdna","html_url":"https://github.com/drdna","followers_url":"https://api.github.com/users/drdna/followers","following_url":"https://api.github.com/users/drdna/following{/other_user}","gists_url":"https://api.github.com/users/drdna/gists{/gist_id}","starred_url":"https://api.github.com/users/drdna/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/drdna/subscriptions","organizations_url":"https://api.github.com/users/drdna/orgs","repos_url":"https://api.github.com/users/drdna/repos","events_url":"https://api.github.com/users/drdna/events{/privacy}","received_events_url":"https://api.github.com/users/drdna/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-06-25T21:10:54Z","updated_at":"2018-06-27T10:20:10Z","closed_at":null,"author_association":"NONE","body":"#### Are you using the latest version of [samtools]\r\n\r\nhaving same issue with samtools 1.3 and 1.8\r\n\r\n #### Please describe your environment.\r\n- OS \r\nLinux 4.4.0-119-generic\r\n- machine architecture\r\nx86_64\r\n- compiler (run `gcc --version` or `clang --version`)\r\ngcc (Ubuntu 5.4.0-6ubuntu1~16.04.9) 5.4.0 20160609\r\n\r\n#### Please specify the steps taken to generate the issue, the command you are running and the relevant output.\r\n\r\nOutput from mpileup is showing CUMULATIVE read depth across the entire reference, not the per-base read depth.  Problem is the same with .bam files produced by bowtie2 and STAR.\r\n\r\nCommand:\r\n\r\nfarman@mac:~$ ./samtools-1.8/samtools mpileup -uvgf BdBar_mito.fasta Po221_S2.BdBar_mito.Aligned.out_sorted.bam  | head -n 200\r\n\r\nOutput:\r\n\r\n[mpileup] 1 samples in 1 input files\r\n<mpileup> Set max per-file depth to 8000\r\n##fileformat=VCFv4.2\r\n##FILTER=<ID=PASS,Description=\"All filters passed\">\r\n##samtoolsVersion=1.8+htslib-1.8\r\n##samtoolsCommand=samtools mpileup -uvgf BdBar_mito.fasta Po221_S2.BdBar_mito.Aligned.out_sorted.bam\r\n##reference=file://BdBar_mito.fasta\r\n##contig=<ID=BdBar_mito,length=35538>\r\n##ALT=<ID=*,Description=\"Represents allele(s) other than observed.\">\r\n##INFO=<ID=INDEL,Number=0,Type=Flag,Description=\"Indicates that the variant is an INDEL.\">\r\n##INFO=<ID=IDV,Number=1,Type=Integer,Description=\"Maximum number of reads supporting an indel\">\r\n##INFO=<ID=IMF,Number=1,Type=Float,Description=\"Maximum fraction of reads supporting an indel\">\r\n##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Raw read depth\">\r\n##INFO=<ID=VDB,Number=1,Type=Float,Description=\"Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)\",Version=\"3\">\r\n##INFO=<ID=RPB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Read Position Bias (bigger is better)\">\r\n##INFO=<ID=MQB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality Bias (bigger is better)\">\r\n##INFO=<ID=BQB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Base Quality Bias (bigger is better)\">\r\n##INFO=<ID=MQSB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)\">\r\n##INFO=<ID=SGB,Number=1,Type=Float,Description=\"Segregation based metric.\">\r\n##INFO=<ID=MQ0F,Number=1,Type=Float,Description=\"Fraction of MQ0 reads (smaller is better)\">\r\n##INFO=<ID=I16,Number=16,Type=Float,Description=\"Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h\">\r\n##INFO=<ID=QS,Number=R,Type=Float,Description=\"Auxiliary tag used for calling\">\r\n##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods\">\r\n"},"comment":{"url":"https://api.github.com/repos/samtools/samtools/issues/comments/400620383","html_url":"https://github.com/samtools/samtools/issues/880#issuecomment-400620383","issue_url":"https://api.github.com/repos/samtools/samtools/issues/880","id":400620383,"node_id":"MDEyOklzc3VlQ29tbWVudDQwMDYyMDM4Mw==","user":{"login":"daviesrob","id":3234562,"node_id":"MDQ6VXNlcjMyMzQ1NjI=","avatar_url":"https://avatars2.githubusercontent.com/u/3234562?v=4","gravatar_id":"","url":"https://api.github.com/users/daviesrob","html_url":"https://github.com/daviesrob","followers_url":"https://api.github.com/users/daviesrob/followers","following_url":"https://api.github.com/users/daviesrob/following{/other_user}","gists_url":"https://api.github.com/users/daviesrob/gists{/gist_id}","starred_url":"https://api.github.com/users/daviesrob/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/daviesrob/subscriptions","organizations_url":"https://api.github.com/users/daviesrob/orgs","repos_url":"https://api.github.com/users/daviesrob/repos","events_url":"https://api.github.com/users/daviesrob/events{/privacy}","received_events_url":"https://api.github.com/users/daviesrob/received_events","type":"User","site_admin":false},"created_at":"2018-06-27T10:20:10Z","updated_at":"2018-06-27T10:20:10Z","author_association":"MEMBER","body":"Unfortunately your example got cut off before the interesting part.  Could you attach it as a file, please?  You may have to save it with a `.txt` suffix or compress it with gzip to get GitHub to accept it.\r\n\r\n Read depth should be reported as `DP`, and as far as I'm aware in VCF output it shows the depth at each given reference position.  Could you explain more about how you think it should be behaving compared to the results that you get?\r\n\r\nAlso, does `bcftools mpileup` work more as you would expect?"}}
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