User: MatthewP

gravatar for MatthewP
MatthewP30
Reputation:
30
Status:
New User
Location:
China
Last seen:
4 hours ago
Joined:
6 months, 2 weeks ago
Email:
m***********@gmail.com

Posts by MatthewP

<prev • 29 results • page 1 of 3 • next >
0
votes
1
answer
104
views
1
answers
Comment: C: How to use snpSift annotate -info option to annotate specific fields of INFO
... Hello, did you missing "annotate" param? My command like java -jar /software/snpEff/SnpSift.jar annotate -info ALLELEID,CLNDN database.gz sample.vcf > result.vcf this works. ...
written 5 days ago by MatthewP30
3
votes
1
answer
104
views
1
answer
How to use snpSift annotate -info option to annotate specific fields of INFO
... Hello, `snpSift` can annotate vcf file from other database vcf, and `-info` option to annotate specific fields. >You can use the -info command line option if you only want select only a subset of fields from db.vcf file. I need some examples to show me how to use `-info` correctly.Example, my `c ...
snpsift annotation written 14 days ago by MatthewP30 • updated 14 days ago by finswimmer7.8k
0
votes
0
answers
111
views
0
answers
Comment: C: Downstream analysis of VCF files obtained from VarScan2
... Hello, `samtools mpileup` can merge multiple files, then use `varscan` to analyse, I don't know if this fits you. ...
written 14 days ago by MatthewP30
1
vote
1
answer
82
views
1
answers
Comment: C: How to change the path so that screen can take the default python path?
... And remember source ~/.bashrc to make it work. ...
written 19 days ago by MatthewP30
0
votes
1
answer
74
views
1
answers
Comment: C: Why snpEff annotation give different names to one same gene?
... Thanks. The annotation source is `GRCH38.86` build-in database from snpEff. I don't have to only keep one of them, I just confusing. ...
written 19 days ago by MatthewP30
1
vote
1
answer
74
views
1
answer
Why snpEff annotation give different names to one same gene?
... Hello, I annotate my vcf with `snpEff` command like: java -Xmx6g -jar snpEff.jar -c configfile GRCH38.86 > result.vcf I checked `ANN` information at `INFO` field in result.vcf and found gene `ND5` has 2 name( `ND5` or `MT-ND5` ) like: C|upstream gene variant|MODIFIER|ND5|ND5|transcript ...
mtdna snpeff written 20 days ago by MatthewP30 • updated 20 days ago by jared.andrews071.6k
0
votes
0
answers
252
views
0
answers
Comment: C: Some questions about call variants for mtDNA using GATK HaplotypeCaller
... Good advice, indeed I need to delete those files by hand. Thanks. ...
written 3 months ago by MatthewP30
0
votes
0
answers
252
views
0
answers
Comment: C: Some questions about call variants for mtDNA using GATK HaplotypeCaller
... Thanks, I used `samtools sort` before until I found `gatk SortSam`. I though this two tools do exactly the same thing. You mean my understanding here is wrong? ...
written 3 months ago by MatthewP30
0
votes
2
answers
541
views
2
answers
Comment: C: Detection of deletion for mitochondrial NGS analysis at position 3107
... So can you get 1 frequency value per variant instead of per site(POS?) I really need frequency for each variant(Clients need mtDNA heterogeneity information). I already find HaplotypeCaller not suite for mtDNA data(because amplicon-based and haploid). ...
written 3 months ago by MatthewP30
2
votes
0
answers
252
views
0
answers
Some questions about call variants for mtDNA using GATK HaplotypeCaller
... Hi everyone. I tried to apply `GATK` pipeline to `amplicon-based` mtDNA sequencing data analyse and found some problems want to ask/discuss with you guys. I sat up my pipeline according this GATK [Best Practice][1]. Here is my pipeline: 1. QC(fastp) 2. mapping ```bwa mem -t 4 -R "@RG\tID..." ...
haplotypecaller gatk mtdna written 3 months ago by MatthewP30

Latest awards to MatthewP

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: 1090 users visited in the last hour