User: Hadi M

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Hadi M30
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New User
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6 months, 2 weeks ago
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2 years ago
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m*********@live.com

Posts by Hadi M

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Fixing BAM file generated without .alt index file during BWA
... Yeah seems like there's no way to fix the BAM file as of now so I have to realign my reads. Cheers. ...
written 11 months ago by Hadi M30
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Fixing BAM file generated without .alt index file during BWA
... 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, ...
bam bwa written 11 months ago by Hadi M30 • updated 11 months ago by Biostar ♦♦ 20
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PASNP genotype data
... 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. ...
snp genotyping written 12 months ago by Hadi M30 • updated 10 months ago by Biostar ♦♦ 20
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VCF: Replacing RefSeq ID to chr in #CHROM
... 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 ...
vcf written 13 months ago by Hadi M30 • updated 11 months ago by devarora290
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Need help with BCFtools annotate; not all information is carried forward
... 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: ...
genome tool written 19 months ago by Hadi M30 • updated 19 months ago by Asaf8.5k
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Using BCFtools to intersect multiple VCF files
... 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 ...
bcftools isec written 23 months ago by Hadi M30
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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 2.0 years ago by Hadi M30
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Counting total variants
... 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 ...
genome variant calling next-gen written 2.0 years ago by Hadi M30 • updated 2.0 years ago by finswimmer14k
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Comment: C: How does bcftools isec do the intersection?
... Thanks for the answers both of you :) Cheers. ...
written 2.0 years ago by Hadi M30
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How does bcftools isec do the intersection?
... 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. ...
bcftools isec written 2.0 years ago by Hadi M30 • updated 2.0 years ago by finswimmer14k

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Popular Question 12 months ago, created a question with more than 1,000 views. For Using BCFtools to intersect multiple VCF files

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