User: cmccabe

gravatar for cmccabe
cmccabe120
Reputation:
120
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Trusted
Location:
Chicago
Last seen:
3 weeks, 4 days ago
Joined:
3 years, 4 months ago
Email:
c******@luriechildrens.org

Posts by cmccabe

<prev • 184 results • page 1 of 19 • next >
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integrate pharmGKB data with annovar
... Is it possible to integrate PharmGKB data with annovar? Have others done this, I am trying to do so and wanted to ask. Thank you :). ...
ngs written 9 weeks ago by cmccabe120 • updated 9 weeks ago by Kevin Blighe6.7k
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Comment: C: calculate average target coverage from bam file
... Thank you both very much :). ...
written 9 weeks ago by cmccabe120
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calculate average target coverage from bam file
... I am trying to calculate the average coverage for each target in a bed file. I tried the below samtools 1.2 command but it gives an error. Is there a better way? Thank you :) targetbed (tab-delimited) chr12 9264962 9265142 chr12:9264962-9265142 A2M chr12 9265945 9266149 chr12:9265945- ...
ngs written 9 weeks ago by cmccabe120 • updated 9 weeks ago by Dan Gaston6.9k
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IGV pileup not showing any reads at any position in bam
... I am not able to figure out why when I load an Ion Torrent bam file into IGV the result is a blank/empty pileup. I routinely run these bam files and have no problems, but am now and not sure why. This is a bam uses a hotspot file, but I am not sure if that is necessary or how to load it properly. ...
ngs written 4 months ago by cmccabe120
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Comment: C: search a large dbsnp file using another most efficiently
... grep -f file1 file2 and awk -F'\t' 'NR==FNR{A[$1];next}$2 in A' also work but are pretty slow on these large files. Thank you :). ...
written 4 months ago by cmccabe120
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search a large dbsnp file using another most efficiently
... I am trying to find the faster (most efficient) tool for searching a very large ~100GB file. The input that is searched for is **file1**, which is just a list of rs#'s in a column (1 per line) --- there may be several hundred ---. **File2** is a sorted list of hg19 HGVS nomenclature for each SNP fr ...
ngs written 4 months ago by cmccabe120
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Comment: C: adding custom INFO tag to vcf
... Thank you very much :). ...
written 5 months ago by cmccabe120
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adding custom INFO tag to vcf
... I am trying to add a few custom INFO tags to a vcf 4.1. The below vcf is what I have in which the last 4 tab-delimited fields (GOOD 103 hom 16 and GOOD 139 het 8) are not defined in the INFO tags. My thought (though probably not the best) was too add 4 INFO tags for these: sed -i '10i\##INFO=\ ...
vcf ngs written 5 months ago by cmccabe120 • updated 5 months ago by Pierre Lindenbaum100k
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Comment: C: hg19 transcript mapping or exon overlap
... Thank you all for your help :) ...
written 5 months ago by cmccabe120
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hg19 transcript mapping or exon overlap
... Is there a tool or script that can map or identify what exon the current version of an hg19 transcript overlaps with? I guess like UCSC genome browser but for just uses the coordinates without visualizing them. Thank you :) For example. Transcript Exon NM_001127222.1 10 ...
ngs written 5 months ago by cmccabe120 • updated 5 months ago by pjalali4610

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Popular Question 4 months ago, created a question with more than 1,000 views. For convert gene name to entrez id
Popular Question 8 months ago, created a question with more than 1,000 views. For convert gene name to entrez id
Popular Question 8 months ago, created a question with more than 1,000 views. For aligned or unaligned bam file
Popular Question 8 months ago, created a question with more than 1,000 views. For ion torrent alignment software
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Student 3.4 years ago, asked a question with at least 3 up-votes. For splice site mutations

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