User: kwanghoon

gravatar for kwanghoon
kwanghoon20
Reputation:
20
Status:
New User
Location:
South Korea/Seoul/Seoul National University Hospital
Last seen:
1 day, 21 hours ago
Joined:
10 months ago
Email:
k********@snu.ac.kr

Posts by kwanghoon

<prev • 28 results • page 1 of 3 • next >
0
votes
0
answers
197
views
0
answers
Comment: C: About GATK4 Mutect2 runtime (Whole Exome seq)
... Thank you. It helps me a lot. Really appreciate your kindness. ...
written 4 weeks ago by kwanghoon20
0
votes
0
answers
197
views
0
answers
Comment: C: About GATK4 Mutect2 runtime (Whole Exome seq)
... (ii) Tumor-only mode This mode runs on a single type of sample, e.g. the tumor or the normal. To create a PoN, call on each normal sample in this mode, then use CreateSomaticPanelOfNormals to generate the PoN. gatk Mutect2 \ -R reference.fa \ -I sample.bam \ - ...
written 5 weeks ago by kwanghoon20
0
votes
0
answers
197
views
0
answers
Comment: C: About GATK4 Mutect2 runtime (Whole Exome seq)
... gatk Mutect2 -R $HG38 --native-pair-hmm-threads 32 -I input.bam -O unfiltered_output.vcf This one ...
written 5 weeks ago by kwanghoon20
0
votes
0
answers
197
views
0
answers
Comment: C: About GATK4 Mutect2 runtime (Whole Exome seq)
... Thank you!! That sounds relief to me.. ...
written 5 weeks ago by kwanghoon20
0
votes
0
answers
197
views
0
answers
Comment: C: About GATK4 Mutect2 runtime (Whole Exome seq)
... That sounds relief to me. I open .vcf file there are no values at column Qual, Filer like below... Is this not normal...? Sorry I'm learning bioinfo, this is very difficult. #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S-140024000-4 chr1 13273 . G C . . AS_SB_TABLE=139,84|63,40;DP=334; ...
written 5 weeks ago by kwanghoon20
8
votes
0
answers
197
views
0
answers
About GATK4 Mutect2 runtime (Whole Exome seq)
... Hi. I'm trying to call variant from WES data by Mutect2. But its running time is 300~400 min per sample. Is it normal or too long? I thought it is too slow so I used "--native-pair-hmm-threads 32" option but it doesn't look like faster. Thanks ...
gatk whole exome sequencing mutect2 written 5 weeks ago by kwanghoon20
1
vote
0
answers
137
views
0
answers
Comment: C: In methylation sequencing, what does BedGraph value stand for?
... Thank you devarora. Then it looks like similar as beta value. ...
written 5 weeks ago by kwanghoon20
2
votes
0
answers
137
views
0
answers
In methylation sequencing, what does BedGraph value stand for?
... I have Methylation capture seq data like BedGraph. BedGraph is called using Bismark tool. I can see 4 column of this file. First column is chromosome, second is start site, third is end site. fourth is values. Does this value stand for methylation value? Like beta value of methylation array? Tha ...
0
votes
1
answer
151
views
1
answers
Comment: C: GATK BaseRecalibrator error.. how do I solve this?
... Wow it worked.... THANK YOU SO SO SO MUCH. I don't know why resource bundle looks like BCF.... Anyway Thank you again!!! ...
written 6 weeks ago by kwanghoon20
0
votes
1
answer
151
views
1
answers
Comment: C: GATK BaseRecalibrator error.. how do I solve this?
... Output of **file resources_broad_hg38_v0_Mills_and_1000G_gold_standard.indels.hg38.vcf** resources_broad_hg38_v0_Mills_and_1000G_gold_standard.indels.hg38.vcf: gzip compressed data, extra field And output of **head resources_broad_hg38_v0_Mills_and_1000G_gold_standard.indels.hg38.vcf** ▒BC&a ...
written 6 weeks ago by kwanghoon20

Latest awards to kwanghoon

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: 1488 users visited in the last hour
_