User: Begonia_pavonina

Reputation:
20
Status:
New User
Location:
Last seen:
4 days, 5 hours ago
Joined:
7 months, 1 week ago
Email:
t**************@protonmail.com

Posts by Begonia_pavonina

<prev • 20 results • page 1 of 2 • next >
0
votes
0
answers
2.7k
views
0
answers
Comment: C: Variant Quality Score Recalibration (Vqsr) For Non-Human Genomes
... Hello Jeremy, I had the same question than Tonyzeng and was wondering how I could filter my variants. However, despite working on a non-model organism, I do have a good-quality list of variants for the species I am working on. So I was wondering if I could maybe make .tranches and .recal files with ...
written 7 days ago by Begonia_pavonina20
0
votes
0
answers
88
views
0
answers
Clustering of SNPs toward same QUAL values
... I am processing VCF files that have been called with FreeBayes version 1.3.1 from target capture data. I have checked the quality score (QUAL phred-scaled quality score) of the variants on my dataset using bcf stats. I found out that most of the SNPs are clustered on specific values of QUAL. For ...
quality freebayes snp variants written 23 days ago by Begonia_pavonina20 • updated 22 days ago by Biostar ♦♦ 20
0
votes
1
answer
101
views
1
answers
Comment: A: How to compare VCF files called from different reference genomes?
... Thanks for your answer igor. I was planning to compare a VCF file mapped to a genome to target-capture VCFs mapped to the baits sequence. Eventually and as you quote, it is easier to map the target-capture dataset to the same reference genome than the first VCF file. Thanks for the help! ...
written 25 days ago by Begonia_pavonina20
1
vote
1
answer
101
views
1
answer
How to compare VCF files called from different reference genomes?
... Hello everyone, How to compare two VCF files called with the same software (FreeBayes), but with completely different reference genomes based on the same specie? The question has been asked here already: https://www.biostars.org/p/355391/#449922 But it seems that LiftoverVcf is made to adjust VC ...
vcf picard alignment freebayes snp written 29 days ago by Begonia_pavonina20
0
votes
1
answer
532
views
1
answers
Comment: C: Comparing VCFs constructed from mapping to different reference genomes
... Something is still unclear to me: Is this tool used to compare VCF files created with different version of the same reference sequence, or can it be used with two completely different reference sequences from the same species? ...
written 29 days ago by Begonia_pavonina20
0
votes
2
answers
15k
views
2
answers
Comment: C: Filters/Quality For Vcf Generated By Freebayes
... Ah, found the answer to my question: Reads marked as duplicates in the BAM file are ignored, but this can be disabled for testing purposes by providing --use-duplicate-reads. ...
written 4 weeks ago by Begonia_pavonina20
0
votes
2
answers
15k
views
2
answers
Comment: C: Filters/Quality For Vcf Generated By Freebayes
... I am a bit confused about the way to filter PCR duplicates. You seem to advice filtering by QUAL but not with the DUP marker. Similarly, in the Freebayes readme page, on paragraph "Calling variants: from fastq to VCF", the tutorial advice to mark duplicates, then to run Freebayes directly. https:/ ...
written 4 weeks ago by Begonia_pavonina20
5
votes
2
answers
274
views
2
answers
GATK 3.8 and GATK 3.7 scripts
... Hello everybody, I am using a pipeline (Paleomix) using the two following scripts found in the GATK folder: GenomeAnalysisTK.jar Picard.jar These scripts do not exist in the last version of GATK (GATK 4), nor in GATK 3.8-1. But I think they are existing in GATK 3.7. Would anyone have this vers ...
gatk version alignment repository written 3 months ago by Begonia_pavonina20 • updated 16 days ago by gethemudo10
0
votes
0
answers
81
views
0
answers
Blast2gff index issue
... Hello everyone, I am trying to use blast2gff, a tool from the mgkit toolkit: https://mgkit.readthedocs.io/en/0.4.1/scripts/blast2gff.html I have used the command to convert blast output in a GFF file: blast2gff blastdb [BLAST_FILE] [GFF_FILE] The error report I got is: IndexError: list ...
gff blast2gff blastn index written 3 months ago by Begonia_pavonina20
0
votes
1
answer
265
views
1
answers
Comment: C: Average depth/coverage before and after PCR duplicates cleanup
... That's very precious information as well ATpoint! I did not make the relation between this flag and the annotations in the BAM file. Definitely going to use Mosdepth. Thanks! ...
written 4 months ago by Begonia_pavonina20

Latest awards to Begonia_pavonina

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: 681 users visited in the last hour