SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 14 of 14
Search took 0.00 seconds.
Search: Posts Made By: trackavinash
Forum: Bioinformatics 01-14-2016, 03:19 PM
Replies: 5
Views: 5,579
Posted By trackavinash
Try regtools -...

Try regtools - https://github.com/griffithlab/regtools, the `junctions extract` command will do this.
Forum: Bioinformatics 01-25-2013, 12:22 PM
Replies: 10
Views: 6,774
Posted By trackavinash
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...
Forum: Bioinformatics 01-07-2013, 10:37 AM
Replies: 2
Views: 2,223
Posted By trackavinash
DeNovoGear - Detecting denovo SNPs and INDELs in trios using NGS data.

Hi all,
I'd like to introduce our tool DeNovoGear,

- Denovogear uses a Bayesian approach to detect denovo SNPs and INDELs in trios using NGS data. It calculates a posterior probability for a...
Forum: Bioinformatics 01-02-2013, 07:49 PM
Replies: 15
Views: 7,158
Posted By trackavinash
I agree with Annotation and snpEff being widely...

I agree with Annotation and snpEff being widely used. I had a chance to use SeattleSeq annotation recently when I had to calculate some Grantham scores -...
Forum: Bioinformatics 01-02-2013, 05:29 PM
Replies: 7
Views: 3,535
Posted By trackavinash
Hi, This is definitely a plug but I'd encourage...

Hi,
This is definitely a plug but I'd encourage you to check out our tool Denovogear which is designed to detect denovo mutations in trios using a Bayesian model that lets you set mutation rate...
Forum: Bioinformatics 10-13-2012, 02:42 PM
Replies: 3
Views: 1,056
Posted By trackavinash
Hi, could you post the exact command that you are...

Hi, could you post the exact command that you are trying to run ? Are you calling SNP's using the mpileup2snp command ?
Forum: Bioinformatics 10-13-2012, 09:22 AM
Replies: 14
Views: 3,444
Posted By trackavinash
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...
Forum: Bioinformatics 10-12-2012, 01:34 PM
Replies: 14
Views: 3,444
Posted By trackavinash
You're absolutely right Justin ! I was trying to...

You're absolutely right Justin ! I was trying to offer Chris a solution based on the fact that he wants to use the VCF from GATK.
Forum: Bioinformatics 10-12-2012, 12:49 PM
Replies: 14
Views: 3,444
Posted By trackavinash
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....
Forum: Bioinformatics 10-11-2012, 11:02 AM
Replies: 14
Views: 3,444
Posted By trackavinash
You could also something like "samtools...

You could also something like

"samtools mpileup -gDf hg19.fa s1.bam s2.bam s3.bam | ./denovogear dnm auto --ped t.ped --bcf -"
Forum: Bioinformatics 10-11-2012, 10:58 AM
Replies: 14
Views: 3,444
Posted By trackavinash
Hi swNGS, Could you make sure that the sample...

Hi swNGS,
Could you make sure that the sample names in the BCF file are the same as specified in the PED file ?
Avinash
Forum: Bioinformatics 06-20-2012, 02:55 PM
Replies: 8
Views: 9,320
Posted By trackavinash
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...
Forum: Introductions 06-20-2012, 02:49 PM
Replies: 1
Views: 914
Posted By trackavinash
Welcome

Welcome Anna !
Forum: Introductions 06-20-2012, 02:44 PM
Replies: 1
Views: 815
Posted By trackavinash
Welcome

Welcome to SeqAnswers John !
Showing results 1 to 14 of 14

 


All times are GMT -8. The time now is 08:12 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO