User: Nandini
Nandini • 810
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Bioinformatician
Develop and maintain pipeline(s) for WES, Targeted gene sequencing, mtDNA NGS analysis
Posts by Nandini
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Answer:
C: hg19 interval list
... maybe not on the gatk bundle site. But probably a [liftover][1] should work ?
[1]: https://genome.ucsc.edu/cgi-bin/hgLiftOver ...
written 6 weeks ago by
Nandini • 810
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... No, we haven't as yet. ...
written 7 weeks ago by
Nandini • 810
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... So is it WGS or WES or targeted ?
...
written 12 weeks ago by
Nandini • 810
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... Have you read the manual ?
The error you get "--file expects a filename prefix; '.ped' and '.map' are automatically appended." is self explanatory.
Please remove the prefix '.ped'
The command should be
plink --file 50_samples --make-bed --out 50_samples_try
...
written 12 weeks ago by
Nandini • 810
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... It will be good if you are able to paste all your commands as we can see the parameters used.
what are the commands for Varscan ? ...
written 12 weeks ago by
Nandini • 810
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... So why did you use a random seed of 50 here ? ...
written 3 months ago by
Nandini • 810
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... That's pretty much the plan - to downsample from 50% to 10% and then check for its read depth.
I was opting for my second option of doing it just once but I was suggested to downsample the same BAM thrice and then take its average read depth ...
written 3 months ago by
Nandini • 810
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... ive edited a bit of my question - so does this help with the reproducibility as well ? ...
written 3 months ago by
Nandini • 810
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... Hello
I am downsampling BAMs down to 10% on control samples to check at what minimum read depth are we able to detect a certain set of SNPs.
What approach do people usually adopt for this
1) downsample the same BAM 3 times with different seed options and then take the average of the read dept ...
written 3 months ago by
Nandini • 810
• updated
7 weeks ago by
shrirambhosle • 30
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... Have you tried [UCSC table browser][1] ?
[1]: https://genome.ucsc.edu/cgi-bin/hgTables?hgsid=711027113_pLhHGH6YmOysUzCgwrfAnskhsBBg ...
written 4 months ago by
Nandini • 810
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