User: victoria_aleks

Reputation:
20
Status:
New User
Location:
Last seen:
36 minutes ago
Joined:
1 year, 4 months ago
Email:
v*************@yahoo.com

Posts by victoria_aleks

<prev • 22 results • page 1 of 3 • next >
0
votes
1
answer
164
views
1
answers
Comment: C: extracting depth info from vcf
... you mean that you want to correct the script? ...
written 7 hours ago by victoria_aleks20
0
votes
1
answer
164
views
1
answers
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 8 hours ago by victoria_aleks20
0
votes
1
answer
164
views
1
answers
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 8 hours ago by victoria_aleks20 • updated 8 hours ago by Pierre Lindenbaum101k
0
votes
1
answer
164
views
1
answers
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 8 hours ago by victoria_aleks20 • updated 8 hours ago by Pierre Lindenbaum101k
0
votes
1
answer
164
views
1
answers
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 1 day ago by victoria_aleks20
0
votes
1
answer
164
views
1
answers
Comment: C: extracting depth info from vcf
... and what if i dont have neither bams nor reference fasta? I only downloaded vcf files from the source ...
written 6 days ago by victoria_aleks20
1
vote
1
answer
164
views
1
answer
extracting depth info from vcf
... Dear all, I need to know the "coverage" of sites in vcf files, but the files i am working with do not contain DP info, only AD. Most of the tools for vcf parcing use DP parameter. I understand that I can use AD to estimate depth, too. Is there any known ways of how to? Will be happy to any help:) ...
vcf ad depth written 7 days ago by victoria_aleks20
0
votes
0
answers
283
views
0
answers
Comment: C: picard MarkDuplicates find EOF problem
... thank you for your advice! the original .bam files i have downloaded from a cancer database, they are kind of old and theoretically could be processed by the old version. I ran 'bedtools intersect' on these files to produce new "intersected" .bam files. That means that my new .bams will have EOF any ...
written 6 months ago by victoria_aleks20
1
vote
0
answers
283
views
0
answers
Comment: C: picard MarkDuplicates find EOF problem
... well, now i have tried to convert my bam into sam, ant then into bam again, and that way MarkDuplicates worked. I guess, I have to repeat this elabortae procedure for each of files... sad :) ...
written 6 months ago by victoria_aleks20
0
votes
0
answers
283
views
0
answers
Comment: C: picard MarkDuplicates find EOF problem
... thank you! is there a way to find out what is wrong then? because all the files are of the size I would expect and when I calculate read depth from these files it looks good and normal. and i have 150 these files... so, really really dont want to trash them and start everything from the beginning:) ...
written 6 months ago by victoria_aleks20

Latest awards to victoria_aleks

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 774 users visited in the last hour