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OpenGene
output bam problem
Output bam file appear unsort region, but Iinput file is sorted bam. I have run dozens of sample, and this sample appear this problem.
cmd: gencore -i XYD0160643_L1.raw_data_mapped.bam -o XYD0160643_L1.consensus.bam -r human_g1k_v37.fasta -b target.bed -j HO0330-XYD0160643_L1.json -h HO0330-XYD0160643_L1.html
I double on that. If the input bam is sorted the output of gencore should also be sorted, otherwise I will have to sort it again that will kill any runtime benefits that gencore brings in comparison with Picard. 'cause sorting is loooooooong and having to sort once again adds many hours.
I check it again，the input bam was sorted. I can share data for you to test for bugs. Probably because of some other problem, it doesn't need to be reordered.
hi:
This is the test data, please check.
Best wishes to you!
------------------ 原始邮件 ------------------ 发件人: "Anton Kulaga"<[email protected]>; 发送时间: 2020年4月17日(星期五) 上午10:38 收件人: "OpenGene/gencore"<[email protected]>; 抄送: "zhengxin"<[email protected]>;"Author"<[email protected]>; 主题: Re: [OpenGene/gencore] output bam problem (#16)
I double on that. If the input bam is sorted the output of gencore should also be sorted, otherwise I will have to sort it again that will kill any benefits that gencore brings in comparison with Picard.
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从QQ邮箱发来的超大附件
HO0330-XYD0160643_L1.raw_data_mapped.bam (701.69M, 2020年05月17日 11:14 到期)进入下载页面：http://mail.qq.com/cgi-bin/ftnExs_download?k=3c3033302d8c1de2c6bdfa0612650b195454520151560d524c07510600480d0e05541e080551091b0251565506000a5202030500344d397e2e0000030448616f2500020604530d053e7c021e46044e69055147516b0858461155571e560454365c&t=exs_ftn_download&code=a0304e96
HO0330-XYD0160643_L1.raw_data_mapped.bam.bai (4.16M, 无限期)进入下载页面：http://mail.qq.com/cgi-bin/ftnExs_download?k=52376265b547dbcd94baab534339541d01560654530e07061e5404575c14520005004f5d0409521f0a550001560f5002525657506515667a7c07515655143e6b77075353550f52016c7b534b1758116d575616043a5407424352064b07580b1c51560b6558&t=exs_ftn_download&code=37bee9f2
The output of gencore is sorted.
If your output is unsorted, please check the version of your gencore, confirm that it is the latest version.
If it's still unsorted. Upload the data here, I will do a test.
If this problem is addressed, please close it.
The output of gencore is sorted.
If your output is unsorted, please check the version of your gencore, confirm that it is the latest version.
If it's still unsorted. Upload the data here, I will do a test.
If this problem is addressed, please close it.
OK. I will check the version of gencore .
- gencore (v0.14.0 or 0.150,) all have this problem, I have send data to your email. Please check.
@sfchen I've just checked the doc, in the docs you actually say "gencore accepts a sorted BAM/SAM with its corresponding reference fasta as input, and outputs an unsorted BAM/SAM." So, you mention unsorted output from sorted input in README. Judging from your commend, you updated it to produce sorted output in the latest version, didn't you? RIght now, I am using my own Docker container ( https://github.com/antonkulaga/biocontainers/blob/master/quality-control/gencore/Dockerfile ), where I use http://opengene.org/gencore/gencore , is the version there the newest one or should I build from github master branch instead there? Actually, the version I have in the docker container tells me it is 0.14.0 while latest official release (both github and anaconda cloud) is 0.13.0, I am somewhat confused