User: venuraherath

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venuraherath20
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Posts by venuraherath

<prev • 20 results • page 1 of 2 • next >
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Comment: C: Variant Calling (Samtools Mpileup): Error
... Thanks again. You were very helpful. Earlier script is still running since its using only one thread though 24 threads are available. Do you deposit your script there at Github? If so please give me the link. So I can look at them and learn more. Have a great day! Venura ...
written 5 weeks ago by venuraherath20
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Comment: C: Variant Calling (Samtools Mpileup): Error
... Thank you so much! It is running now. Regarding `bcftools call` ; I have received VCF files generated via original workflow (as given in the old script). Now I am confused. Do you think it is better to dump those VCF files and re do those samples as well, (esp since dif version of tools were used ...
written 5 weeks ago by venuraherath20
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Comment: C: Variant Calling (Samtools Mpileup): Error
... bcftools mpileup -Ou -a FORMAT/DP -d 8000 -f GCF_000002315.5_GRCg6a_genomic.fna FCC717NANXX-wHAIPI020726-60.bam > FCC717NANXX-wHAIPI020726-60.out [mpileup] 1 samples in 1 input files ...
written 5 weeks ago by venuraherath20
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Comment: C: Variant Calling (Samtools Mpileup): Error
... Oh, got it. Thank you so much. - Yes I will use -Ou . Most of the examples available are based on `samtools mpileup` not `bcftools mpileup`. - Actually what i wanted there was was to keep read depth for each sample. So I will use `-a FORMAT/DP` - I will move `-d 8000` before `-f` `bcf ...
written 6 weeks ago by venuraherath20
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Comment: C: Variant Calling (Samtools Mpileup): Error
... If I use the following will it do the trick? Thanks. bcftools mpileup -u -t DP -f -d 8000 > [mpileup] 1 samples in 1 input files ...
written 6 weeks ago by venuraherath20
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Comment: C: Variant Calling (Samtools Mpileup): Error
... Are your referring to <> between output files? This is just the template. I used real file name and didnt include <>. except for ` Set max per-file depth to 8000^C` ...
written 6 weeks ago by venuraherath20
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Variant Calling (Samtools Mpileup): Error
... Hi, I am trying to update a variant calling script came from the predecessors. I am getting the error "bash: mpileup : No such file or directory" Following are the contents of the old script; samtools mpileup -uD -f > [mpileup] 1 samples in 1 input files Set max per-file depth to 8000^ ...
variant calling samtools bcftools mpileup written 6 weeks ago by venuraherath20
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Comment: C: Best way of Merging Multiple Lanes generated by HiSeq 2000, index BAM or VCF?
... Awesome! Thank you so much! Have a Great Day! Venura ...
written 6 weeks ago by venuraherath20
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Comment: C: Best way of Merging Multiple Lanes generated by HiSeq 2000, index BAM or VCF?
... Thank You! I am going to use `merge` in SAMtools for merging index bam files. Do I need to keep bai files (this case 3) in the same folder as well? After merging do i need to index it again? ...
written 6 weeks ago by venuraherath20
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Best way of Merging Multiple Lanes generated by HiSeq 2000, index BAM or VCF?
... Hi Folks, I just want to make sure I am on the right track. I have paired reads coming from three Lanes per each sample. Following is what I did so far; I mapped reads to reference genome using BWA in SAM tools. Now I have indexed BAM files (3 per each sample). I am thinking of merging bam files ...
wgs sam mapping illumina hiseq written 6 weeks ago by venuraherath20

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Scholar 8 months ago, created an answer that has been accepted. For A: Installing IGV on Bio-linux 8 - Installing All Dependancies At Once

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