User: shubhra.bhattacharya
shubhra.bhattacharya • 40
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- 8 months, 4 weeks ago
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Posts by shubhra.bhattacharya
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... You can look into mutect: https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_cancer_m2_MuTect2.php ...
written 4 weeks ago by
shubhra.bhattacharya • 40
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... Hi!
Can someone tell me is there a way by which I can perform PCA on variants and plot them as well?
I tried to read the PLINK pca page but I cannot make my way through it.
My input will be .vcf file.
Thanks!! ...
written 6 weeks ago by
shubhra.bhattacharya • 40
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... https://groups.google.com/forum/#!msg/delly-users/6Mq2juBraRY/Pj4NVGdvHAAJ ...
written 7 weeks ago by
shubhra.bhattacharya • 40
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... I have the same issue as indicated in the link below. Specially how co-ordinates are mapped during translocation events.
https://www.biostars.org/p/328924/
...
written 8 weeks ago by
shubhra.bhattacharya • 40
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... Yes I specified the ploidy as haploid. ...
written 8 weeks ago by
shubhra.bhattacharya • 40
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... Hello guys!
was this problem resolved I am getting the same issue now. ...
written 4 months ago by
shubhra.bhattacharya • 40
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... Dear all,
Although this question may seem a bit trivial but can someone please explain what the GT field (0,1,2) imply in case of haploid organism.
I called SNP's using Haplotype caller.
A typical entry is indicated below:
NW_001091929.1 14514 . T A 56.12 . AC=0;AF ...
written 5 months ago by
shubhra.bhattacharya • 40
• updated
3 months ago by
Biostar ♦♦ 20
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... Hello everyone,
I want to get a hands-on with learning transcriptomics.
Can someone please guide me as to where I can find data set to learn transcriptomics.
I am a beginner to the field and do not have access to any data set to utilise what I read in papers. ...
written 5 months ago by
shubhra.bhattacharya • 40
• updated
5 months ago by
svlachavas • 480
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... 5891581 chrMT 16129 G A
5891582 chrMT 16129 G A
5891583 chrMT 16179 CAA C
5891584 chr1 3088286013 AAA CCC
5891585 chrMT 16182 A C
5891586 chrMT 16183 A C
5891587 chrMT 16186 C T
5891588 chrMT 16188 C T
5891589 chrMT 16189 T C
This is the output of the command.
The chr1 is just dropping by in b/w t ...
written 6 months ago by
shubhra.bhattacharya • 40
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... While using tabix I encounter the following error.
> [ti_index_core] the chromosome blocks not continuous at line 5891584,
> is the file sorted? [pos 1]
Command:
/data/ngs/programs/tabix-0.2.6/tabix -p vcf SRR12954_1.fastq.gz_20180228112323.GRCH38.vcf.gz
I have zipped the vcf file using bg ...
written 6 months ago by
shubhra.bhattacharya • 40
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