User: MatthewP

gravatar for MatthewP
MatthewP10
Reputation:
10
Status:
New User
Location:
China
Last seen:
2 days, 16 hours ago
Joined:
4 months, 3 weeks ago
Email:
m***********@gmail.com

Posts by MatthewP

<prev • 23 results • page 1 of 3 • next >
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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 6 weeks ago by MatthewP10
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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 6 weeks ago by MatthewP10
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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 6 weeks ago by MatthewP10
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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 6 weeks ago by MatthewP10
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Comment: C: Detection of deletion for mitochondrial NGS analysis at position 3107
... Hey Nandini, I used `mPileup + varscan` as you suggested. I still have some questions/problems want to ask you: 1. Did you use `varscan` `mpileup2cns` command? I used this and I found this only call one mutation frequency for me each position even there are **more than 1 variant** at that site. [C ...
written 6 weeks ago by MatthewP10
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How to apply GATK on mtDNA sequencing data?
... Hello, everyone. I sat up a mtDNA pipeline using `samtools mpileup` + `varscan2` to do variant call. However this pipeline has one problem when there is more than one variants in same site, I can only get only one **frequency** value, I need one frequency data per variant because mtDNA **heterogenei ...
gatk mtdna written 7 weeks ago by MatthewP10
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Comment: C: How to download dataset from MITOMAP?
... Thanks, that's exactly what I want. ...
written 3 months ago by MatthewP10
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Comment: C: Modify IOT formated VCF by the most frequent variant
... Hello, this is not a valid VCF format, check [here][1] for the right VCF format. [1]: https://samtools.github.io/hts-specs/VCFv4.2.pdf ...
written 3 months ago by MatthewP10
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Comment: C: Removing Duplicates before aligning
... Wow, thanks for your answer. I also have some amplicon-based data and I didn't do mark duplicates job because [fastp][1] shows the duplication rates is more than 96%. Now I know I should use vsearch to mark duplicates. [1]: https://www.biorxiv.org/content/early/2018/03/01/274100 ...
written 3 months ago by MatthewP10
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Comment: C: How to download dataset from MITOMAP?
... Ok, that's what I am doing, thanks for you reply! ...
written 3 months ago by MatthewP10

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