User: ajuiwl

gravatar for ajuiwl
ajuiwl30
Reputation:
30
Status:
New User
Location:
Last seen:
2 months, 1 week ago
Joined:
6 months, 2 weeks ago
Email:
a**********@hotmail.com

Posts by ajuiwl

<prev • 11 results • page 1 of 2 • next >
0
votes
1
answer
87
views
1
answers
Comment: C: Does it make sense to repeat the assembly step in variant calling?
... Thank you for your answer!! ...
written 10 weeks ago by ajuiwl30
1
vote
1
answer
87
views
1
answer
Does it make sense to repeat the assembly step in variant calling?
... Since the mapping step is non-deterministic, would it make sense to generate another BAM file with the same FASTQ file and same config with the objective of analyzing if a new variant is detected? Thank you very much ...
variant calling written 10 weeks ago by ajuiwl30 • updated 10 weeks ago by Devon Ryan89k
1
vote
1
answer
219
views
1
answer
Consensus VCF file from several variant callers
... Hi all, I want to do a consensus VCF file with only the variants that have been called by two variant callers. The problem is that for the same variant the INFO and FORMAT columns of the VCF files show different values, this is to say: GATK shows the variant with DP, MQ, FS values that differ from t ...
vcf variant calling freebayes gatk written 4 months ago by ajuiwl30 • updated 4 months ago by Pierre Lindenbaum119k
1
vote
2
answers
449
views
2
answers
Comment: C: Filter VCF with bash commands
... That is true, I just found that there are some variants in the vcf that didn't have INFO about QD nor DP, and the commands I did didn't considered this. So I agree with you using already made software in that sense. In addition I will add that sometimes you are working in a server that requires the ...
written 5 months ago by ajuiwl30
0
votes
2
answers
449
views
2
answers
Comment: C: Filter VCF with bash commands
... Some programs change the way variants are normalized, the header, require installations, require dependencies, and other issues that bash code can avoid, moreover I have more control over what I do. ...
written 5 months ago by ajuiwl30
0
votes
2
answers
449
views
2
answers
Comment: C: Filter VCF with bash commands
... This answer does not consider decimal positions, in the way that 8.1 won't be kept. ...
written 5 months ago by ajuiwl30
2
votes
2
answers
449
views
2
answers
Answer: A: Filter VCF with bash commands
... Thank you for your answers, I found the way of doing it with: grep -Po 'QD=.*' $FILE | cut -d";" -f1 | sed -r 's/[QD\=]//g' | paste -d'\t' $FILE - | awk 'BEGIN{OFS="\t"}{if ($11>8) {$11=""; print}}' ...
written 5 months ago by ajuiwl30
10
votes
2
answers
449
views
2
answers
Filter VCF with bash commands
... Hi, I have been trying to manually filter a vcf file by QD score, but I have not been able to do it properly. I thought of using awk and indicate that a specific field has a value greater than 8 (that is the value I want to filter it), but I have records where the QD variable does not occupy the sam ...
vcf grep awk bash written 5 months ago by ajuiwl30 • updated 5 months ago by dariober10.0k
1
vote
1
answer
219
views
1
answer
DP and DP at site do not match using only 1 sample in VCF
... I only used 1 sample with BWA and GATK4 germinal variants. The final VCF has variants like this: 1 230451938 . G A 18.25 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.967;ClippingRankSum=0.00;DP=20;ExcessHet=3.0103;FS=4.771;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.0 ...
vcf variant calling gatk written 6 months ago by ajuiwl30
0
votes
1
answer
241
views
1
answers
Comment: C: 4/6 genotype in VCF
... Thank you for the answers, the fact that I do not understand is how the calling in a diploid genome can yield variants with more than 3 alternative alleles (reference, copy 1 and copy 2) if only 1 sample is being used, is that possible? ...
written 6 months ago by ajuiwl30

Latest awards to ajuiwl

Scholar 5 months ago, created an answer that has been accepted. For A: Filter VCF with bash commands

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 755 users visited in the last hour