Forum: Bioinformatics
01-14-2016, 04:19 PM
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Replies: 5
Views: 5,778
Try regtools -...
Try regtools - https://github.com/griffithlab/regtools, the `junctions extract` command will do this.
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Forum: Bioinformatics
01-25-2013, 01:22 PM
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Replies: 10
Views: 6,858
Hi Shuang,
Just curious, did you finally...
Hi Shuang,
Just curious, did you finally accomplish this ? I'm trying to call het SNPs from individual chromatograms but Polyphred seems to assemble multiple reads and then create a consensus...
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Forum: Bioinformatics
01-07-2013, 11:37 AM
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Replies: 2
Views: 2,259
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Forum: Bioinformatics
01-02-2013, 08:49 PM
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Replies: 15
Views: 7,249
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Forum: Bioinformatics
01-02-2013, 06:29 PM
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Replies: 7
Views: 3,617
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Forum: Bioinformatics
10-13-2012, 03:42 PM
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Replies: 3
Views: 1,086
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Forum: Bioinformatics
10-13-2012, 10:22 AM
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Replies: 14
Views: 3,497
Hi Chris,
To get a vcf output try this,
...
Hi Chris,
To get a vcf output try this,
"samtools mpileup -gDf $ref_genome $bam1 $bam2 $bam3 | denovogear dnm XD --ped trio.ped --bcf -
--output o1.vcf"
I will update the README to show...
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Forum: Bioinformatics
10-12-2012, 02:34 PM
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Replies: 14
Views: 3,497
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Forum: Bioinformatics
10-12-2012, 01:49 PM
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Replies: 14
Views: 3,497
Hi Chris,
DeNovoGear takes in BCF files as...
Hi Chris,
DeNovoGear takes in BCF files as input, so you have to find some way of converting the GATK vcf's to BCF. There was some talk that the VCF to BCF convertor in bcftools was not perfect....
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Forum: Bioinformatics
10-11-2012, 12:02 PM
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Replies: 14
Views: 3,497
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Forum: Bioinformatics
10-11-2012, 11:58 AM
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Replies: 14
Views: 3,497
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Forum: Bioinformatics
06-20-2012, 03:55 PM
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Replies: 8
Views: 9,408
Hi Everyone! Thanks to all those in this thread...
Hi Everyone! Thanks to all those in this thread for their invaluable help.. I got it installed today.. Also if you don't want to copy the .dylib to your current folder you can do something like this...
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Forum: Introductions
06-20-2012, 03:49 PM
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Replies: 1
Views: 934
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Forum: Introductions
06-20-2012, 03:44 PM
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Replies: 1
Views: 840
Welcome
Welcome to SeqAnswers John !
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