tag:blogger.com,1999:blog-14688252.post8510889206515984322..comments2024-02-16T10:17:12.310+01:00Comments on YOKOFAKUN: First rule of Bioinfo-ClubPierre Lindenbaumhttp://www.blogger.com/profile/13765837643388003852noreply@blogger.comBlogger6125tag:blogger.com,1999:blog-14688252.post-246962774244612142011-01-18T06:27:09.677+01:002011-01-18T06:27:09.677+01:00I believe more than half of people are using comma...I believe more than half of people are using command lines. JSON/XML will utterly ruin their lives. Also in the world of NGS, efficiency is often of the first priority. A few of us increasingly feel VCF is not efficient to parse. JSON/XML will only make this worse.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-14688252.post-45614739588767667112010-07-01T11:50:29.715+02:002010-07-01T11:50:29.715+02:00My bugbear with these formats is that the embedded...My bugbear with these formats is that the embedded structured data should be done in JSON, not some ad hoc format. In vcf, you have<br /><br /><br />GT:DP:GL:GQ 1/1:11:-28.60,-3.15,-0.15:30.00<br /><br /><br />In GFF3 you have<br /><br />ID=blah;Parent=foo<br /><br /><br />If you are going to embed data in a single column, use JSON. i.e.:<br /><br /><br />{'GT': '1/0', 'James Casbonhttps://www.blogger.com/profile/06969939728038499217noreply@blogger.comtag:blogger.com,1999:blog-14688252.post-61940863682259505162010-05-25T15:39:53.293+02:002010-05-25T15:39:53.293+02:00Just one tiny remark:
cat file.vcf | java -jar vc...Just one tiny remark:<br /><br /><b>cat file.vcf | java -jar vcf2xml.jar > vcf.xml</b><br />is considered bad Un*x style, indeed there is an unnecessary call to <b>cat</b>...<br /><br />The same can be done with pure shell as<br /><b>java -jar vcf2xml.jar < file.vcf > vcf.xml</b><br /><br />SylvainSylvainhttp://contraintes.inria.fr/~soliman/noreply@blogger.comtag:blogger.com,1999:blog-14688252.post-63248748241180928712010-05-20T15:16:30.488+02:002010-05-20T15:16:30.488+02:00thanks for this post it. I find it very educationa...thanks for this post it. I find it very educational and a good example of XML use.Anonymoushttps://www.blogger.com/profile/12551269207203881043noreply@blogger.comtag:blogger.com,1999:blog-14688252.post-54663810481309915202010-05-20T09:36:53.927+02:002010-05-20T09:36:53.927+02:00I don't meant that the NGS softwares should ou...I don't meant that the NGS softwares should output some XML but I needed a file format where I could add some informations about the mutations. So let's say that's VCF is OK (it is compact, sortable, etc..) but I've only created a new kind of file to manage my data.Pierre Lindenbaumhttps://www.blogger.com/profile/13765837643388003852noreply@blogger.comtag:blogger.com,1999:blog-14688252.post-35476650598297503592010-05-20T09:30:48.105+02:002010-05-20T09:30:48.105+02:00what about coding those informations in another fi...what about coding those informations in another file? or in a table?<br /><br />VCF is designed to store only genotypes and raw informations, from a certain point of view this could be an advantage.dalloliogmhttps://www.blogger.com/profile/11230528124875348719noreply@blogger.com