User: sara_wasl

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sara_wasl0
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Posts by sara_wasl

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Comment: C: read depth using samtools
... Thanks a lot for your help, I will try that :) ...
written 6 weeks ago by sara_wasl0
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read depth using samtools
... Hello all, I'm using samtools in order to get the depth of a file called file.bam, but the output I have is like this: samtools depth file.bam > output.txt 11 88911833 2 11 88911834 2 11 88911835 2 I understand that the first column is the name of the reference sequence, the s ...
samtools depth written 6 weeks ago by sara_wasl0 • updated 6 weeks ago by benformatics500
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Comment: C: Download Tumor VCF files
... I applied but even though the vcf files I cannot download them ...
written 12 weeks ago by sara_wasl0
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Comment: C: Download Tumor VCF files
... So, what's the solution? ...
written 12 weeks ago by sara_wasl0
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Download Tumor VCF files
... Hi all, Could anyone please guide me to any databases or websites that I can downloads tumor VCF files from, I tried different databases but it's very difficult and some of them require to register and when I registered the data locked (I cannot downloads anything) Any help with that please? ...
vcf varients written 12 weeks ago by sara_wasl0 • updated 12 weeks ago by jared.andrews071.8k
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Pathogenicity score ranges
... Hello all, Could you please help me to know the pathogenicity score ranges for those tools: - CADD - MutationTaster - VEST3 - fathmm I'm asking because I didn't see their score ranges officially on their websites, so I want to make sure about their scores. Any help will be appreciated, thanks ...
score tool pathogenicity written 3 months ago by sara_wasl0
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Comment: C: Mutation count in multi-sample vcf file
... Sorry but that what I understand from your post above with: $ curl -s -k "https://raw.github.com/arq5x/gemini/master/test/test4.vep.snpeff.vcf" |\ java -jar dist/groupbygene.jar ...
written 4 months ago by sara_wasl0
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Comment: C: Mutation count in multi-sample vcf file
... This is more logical, I'm thinking that the command you provided not correct: file.vcf |\ java -jar dist/groupbygene.jar This is what I have been tried and give me the error. ...
written 4 months ago by sara_wasl0
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Comment: C: Mutation count in multi-sample vcf file
... See here: /................./ ...
written 4 months ago by sara_wasl0
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Comment: C: Mutation count in multi-sample vcf file
... The input file was the one after annotated using SnpEff, This is what I got for **grep -m1 CHROM myfile.ann.vcf** : #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT LIBRARY_NAME=S2000 2:LIBRARY_NAME=S2000 3:LIBRARY_NAME=S2000 4:LIBRARY_NAME=S2000 5:LIBRARY_NAME=S2000 6:LIBRARY_NAME=S2000 7:LIBRARY ...
written 4 months ago by sara_wasl0

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