User: cmccabe

gravatar for cmccabe
cmccabe160
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Chicago
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1 month, 1 week ago
Joined:
3 years, 11 months ago
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c******@luriechildrens.org

Posts by cmccabe

<prev • 194 results • page 1 of 20 • next >
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Comment: C: bcftools split and filter variants in vcf
... Thank you very much :). ...
written 3 months ago by cmccabe160
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bcftools split and filter variants in vcf
... I use bcftools norm to split and left-normalize variants (like the line in file). After norm the variant is split correctly and annotated, my question is can the AF tag be used to filter out AF= below 20% in the command or is there another? So in this case the first split vatiant is filtered out. Th ...
ngs bcftools written 3 months ago by cmccabe160 • updated 3 months ago by Kevin Blighe19k
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Comment: C: NGS variant prioritization tools/script
... Are there additional tools/resources that you recommend? Thank you :). ...
written 4 months ago by cmccabe160
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bedtools coverage bed
... The bedtools 2.25 command I use for coveregeBed is: coverageBed -d -g genomefile.txt -a target.bed -b input.bam > output.txt That works for the vast majority of bam files, however when each bam exceeds 60 million mapped reads (~60GB) the run errors. I have been reading about recent memory l ...
bedtools ngs written 4 months ago by cmccabe160 • updated 4 months ago by Alex Reynolds24k
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Comment: C: NGS variant prioritization tools/script
... The below awk is an example of what I was thinking but not really sure. Thank you :). awk ' BEGIN { # Set input and output field separators: FS = OFS = "\t" # Create list of needed field headers: nfh["FuncrefGene"] nfh["GeneDetailrefGene"] ...
written 4 months ago by cmccabe160
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Comment: C: NGS variant prioritization tools/script
... Using the data within the annovar annotation, for example population frequency and clinvar are used in the classifier but maybe I need to expand on that and use inheritance or phenotype? Maybe another column with the score. Just an idea not even sure if I am on the right track though. I wrote an awk ...
written 4 months ago by cmccabe160
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NGS variant prioritization tools/script
... I am looking for a tool or script to perform variant prioritization on annotated data from annovar. Currently, I have a script that will classify based on information in the annotation but would like to add a priority score or call to the data as well. I know that is much detail but I guess I am loo ...
ngs written 4 months ago by cmccabe160 • updated 4 months ago by genomax48k
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Comment: A: add coordinates to line of output extracted from vcf
... Amazing, works great.... thank you, really nice tool :) ...
written 6 months ago by cmccabe160
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Comment: C: add coordinates to line of output extracted from vcf
... I was not aware bcftools could do this. I ran: bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%SAMPLE=%GT]\n' NA12878s5.vcf.gz | head 5 chr1 949608 G A MEC1=0/1 chr1 949654 A G MEC1=1/1 chr1 977330 T C MEC1=0/1 chr1 981931 A G MEC1=0/1 chr1 982994 T C MEC1=0/1 Can the raw ...
written 6 months ago by cmccabe160
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add coordinates to line of output extracted from vcf
... I am trying to extrapolate/convert variants from a vcf file to genotype. I am close but can not seem to add the chr and start of each line to the output. Maybe there is a better way? Thank you :). #!/usr/bin/perl # execute perl script use strict; use warnings; use Vcf; m ...
vcf genotype written 6 months ago by cmccabe160

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