User: Hadi M
Hadi M • 30
- Reputation:
- 30
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- New User
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- Last seen:
- 1 month, 3 weeks ago
- Joined:
- 1 year, 2 months ago
- Email:
- m*********@live.com
Posts by Hadi M
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... Yeah seems like there's no way to fix the BAM file as of now so I have to realign my reads. Cheers. ...
written 8 weeks ago by
Hadi M • 30
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... Hi everyone,
I generated a BAM file after aligning my NGS reads against the reference genome using BWA. My reference genome contains ALT contigs but I did not supply the .alt index file during alignment. I know I can just do the alignment again with the .alt index file but before I proceed to that, ...
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... Hi,
I would like to know if there is an alternative way to download the genotyping data from the PAN-Asian SNP database (http://www4a.biotec.or.th/PASNP)? I cannot register nor contact the website owner and I need the file for my pc and admixture analysis.
Many thanks. ...
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... Hi everyone,
I recently downloaded the latest [dbSNP VCF][1] and when opening the file, I noticed the #CHROM column is filled with RefSeq ID instead of chr1, chr2 or so on. Here is how the VCF looks like:
#CHROM POS ID REF ALT QUAL FILTER INFO
NC_000001.11 10019 rs775809821 TA ...
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... Hi everyone,
I have a custom tab delimited annotation file that I used to annotate a VCF file using *bcftools annotate*. It worked just fine but the only problem is that if there are multiple hits on a particular position, only the first information is carried into the VCF file. Here's an example:
...
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... Hi all,
I have 5 VCF files (A, B, C, D, and E) and I want to obtain all the variants shared by A and B only (not found in C, D, and E). I used BCFtools to do this and output all the positions. When I examined the variants using IGV, I still find variants that are not shared exclusively between A an ...
written 13 months ago by
Hadi M • 30
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Comment:
C: Counting total variants
... Thank you very much both of you and thanks for the feedback at the end [ATpoint][1], will keep that in mind :). Cheers
[1]: https://www.biostars.org/u/25721/ ...
written 14 months ago by
Hadi M • 30
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... Hello,
I am curious of how normally variant researchers count their variants. The full assembly of GRCh38 contains the primary assembly (chromosome 1:22, X and Y), mitochondrial genome, some patches and alternate locus. After variant calling, do they only count the variants from the entire assembly ...
written 14 months ago by
Hadi M • 30
• updated
14 months ago by
finswimmer ♦ 13k
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... Thanks for the answers both of you :) Cheers. ...
written 14 months ago by
Hadi M • 30
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... Hi all,
I am just wondering how does bcftools isec do the intersection? Does it take account of other headers, e.g. REF and ALT, or it just look at the CHROM and POS and consider it as intersection despite the REF and ALT?
Thanks and cheers. ...
written 15 months ago by
Hadi M • 30
• updated
15 months ago by
finswimmer ♦ 13k
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For Using BCFtools to intersect multiple VCF files
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