User: erarroji

gravatar for erarroji
erarroji0
Reputation:
0
Status:
New User
Last seen:
3 days, 1 hour ago
Joined:
2 months, 2 weeks ago
Email:
e*******@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by erarroji

<prev • 7 results • page 1 of 1 • next >
0
votes
1
answer
134
views
1
answers
Comment: C: Trouble with best practices
... Thank you, I will trust GATK. The variant calling was made with the same tool (Mutect 2), I only changed the markduplicates tools. In all cases y used default values, could that be what is generating troubles? ...
written 12 days ago by erarroji0
0
votes
1
answer
134
views
1
answers
Comment: C: Trouble with best practices
... Thank you, I did checked the duplicates, they were as fraction and also I checked it with samtools flagstat making the calculation with the raw values. ...
written 12 days ago by erarroji0
3
votes
1
answer
134
views
1
answer
Trouble with best practices
... Hi I'am new with all NGS tools, I tried to follow best practices workflow for my exome reads from tumor samples: I align with bwa mem, sort with samtools, mark duplicates and recalibrated bases with GATK 4 and finally call variants with Mutect 2. Although the software run successfully I noticed tha ...
bioinformatics ngs wes samtools gatk written 12 days ago by erarroji0
0
votes
0
answers
171
views
0
answers
Comment: C: Picard CollectHsMetrics malfunctioning
... I really thank you it has been really useful ...
written 11 weeks ago by erarroji0
0
votes
0
answers
171
views
0
answers
Comment: C: Picard CollectHsMetrics malfunctioning
... Already did. Coverage depth, mean coverage and off target. ...
written 11 weeks ago by erarroji0
0
votes
0
answers
171
views
0
answers
Comment: C: Picard CollectHsMetrics malfunctioning
... Thank you Pierre, i've been struggling with this all week. It is exactly the same mistake, but my input files are ok. Could you suggest me another software for calculate the metrics? Thank you ...
written 11 weeks ago by erarroji0
1
vote
0
answers
171
views
0
answers
Picard CollectHsMetrics malfunctioning
... I tried to run CollectHsMetrics, this is my command: java -jar /picard.jar CollectHsMetrics \ I=190.sortedDeDup.bam \ O=190_hs_metrics.txt \ R=ucsc.hg19.fasta \ BAIT_INTERVALS=AgilentSSV6_bait_list.interval_list \ TARGET_INTERVALS=V6SureSelect/AgilentSSV6_targets_list.interval_list it works ok unt ...
picard ngs wes collecthsmetrics written 11 weeks ago by erarroji0 • updated 11 weeks ago by Pierre Lindenbaum104k

Latest awards to erarroji

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: 540 users visited in the last hour