User: victoria_aleks

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Posts by victoria_aleks

<prev • 27 results • page 1 of 3 • next >
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Comment: C: extracting depth info from vcf
... ok, at the end we had to write our own script:) ...
written 4 months ago by victoria_aleks30
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Comment: C: Filreing vcf files not giving any results
... hi Abdul, did you solve the problem?:) ...
written 4 months ago by victoria_aleks30
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Comment: C: extracting depth info from vcf
... but also: can I extract exactly AD values, not only DP?? I want to know how many reads contain ref and how many contain alt nucleotides. ...
written 4 months ago by victoria_aleks30
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Comment: C: extracting depth info from vcf
... thank you a lot:) it all finally seem to work now! ...
written 4 months ago by victoria_aleks30
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Comment: C: extracting depth info from vcf
... now it worked:) as I understand the script summated AD for ref and alt and wrote it into DP parameter. but now i try to use vcftools to extract this DP (for example, --depth or --geno-depth) and it reports on 'missing entries'. and i still cannot use gatk, i think, as i have only vcf files, no fasta ...
written 5 months ago by victoria_aleks30
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Comment: C: extracting depth info from vcf
... you mean that you want to correct the script? ...
written 5 months ago by victoria_aleks30
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Comment: C: extracting depth info from vcf
... its a "wrapper", as our IT guy likes to use short words:) so, "java -jar ..." is included in "vcffilterjdk" ...
written 5 months ago by victoria_aleks30
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Comment: C: extracting depth info from vcf
... i see:) honestly i repeated exactly what you wrote. except, first i ran awk command (i checked the resulting file, and DP appeared there. only: i do not understand why do I need incorporate DP in the header if I want to use AD anyway?). then I set this awk-mdified file as the input for vcffilterjdk ...
written 5 months ago by victoria_aleks30 • updated 5 months ago by Pierre Lindenbaum106k
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Comment: C: extracting depth info from vcf
... :) basically my question was: does it worth it to write a script myself or better not to mess? anyway, the error is: 2 errors [SEVERE][InMemoryCompiler]compile.call() failed for custom class VcfFilterJdkCustom887993132 java.lang.RuntimeException: compile.call() failed for custom class VcfFilter ...
written 5 months ago by victoria_aleks30 • updated 5 months ago by Pierre Lindenbaum106k
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Comment: C: extracting depth info from vcf
... thank you very much. unfortunately vcffilterjdk constantly gives errors, in my hands :) Is it possible just write a home-made script to extract AD values for each line in vcf-file? I read that its better not to mess with vcf parcing and rather use the ready software. but right now it seems easier ju ...
written 5 months ago by victoria_aleks30

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