User: olavur

gravatar for olavur
olavur100
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Tórshavn, Faroe Islands
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5 months ago
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Posts by olavur

<prev • 51 results • page 1 of 6 • next >
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Comment: C: Is there a tool or method for phasing a VCF based on an already phased BAM?
... Can you email me at olavur(at)fargen.fo? Discussing this in the comments is becoming cumbersome. ...
written 20 months ago by olavur100
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Comment: C: Is there a tool or method for phasing a VCF based on an already phased BAM?
... If you want to look at the phase blocks in IGV, you can use the `whatshap stats [VCF] --gtf [GTF]` command (see [here](https://whatshap.readthedocs.io/en/latest/guide.html#gtf-with-haplotype-blocks)). ...
written 20 months ago by olavur100
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Comment: C: Is there a tool or method for phasing a VCF based on an already phased BAM?
... I'm trying it just now, but don't have any results yet. I doubt WhatsHap looks at the "10X PHASING INCONSISTENT" tag, it is specific to 10x and WhatsHap accepts any VCF phased by any method. You could try to visualize the haplotype/phase blocks in IGV. The fact that the variant has read coverage d ...
written 20 months ago by olavur100
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Comment: C: Is there a tool or method for phasing a VCF based on an already phased BAM?
... I'm looking into the paper and the docs. It sounds really promising, thank you. ...
written 23 months ago by olavur100
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Comment: C: Is there a tool or method for phasing a VCF based on an already phased BAM?
... Will this take advantage of the fact that my BAM is already phased (each read is assigned to a haplotype)? ...
written 23 months ago by olavur100
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Comment: C: Is there a tool or method for phasing a VCF based on an already phased BAM?
... This tool does not do the task I need. I edited the question with a clarification. ...
written 23 months ago by olavur100
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Comment: C: Is there a tool or method for phasing a VCF based on an already phased BAM?
... This tool does not do the task I need. I edited the question with a clarification. ...
written 23 months ago by olavur100
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Is there a tool or method for phasing a VCF based on an already phased BAM?
... I have some BAM files where the reads are phased, such that each read belongs to haplotype 1 or 2 (or NA if the read isn't phased). Next I call variants in these BAMs, and obtain an unphased VCF. The question is: is there a method, algorithm, software, anything, that allows me to phase the variants ...
vcf haplotype phasing bam written 23 months ago by olavur100
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Comment: C: Iterating through paired-end reads in samtools / pysam
... Thank you, an elegant solution. Have you used this method a lot? ...
written 2.1 years ago by olavur100
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Comment: C: Iterating through paired-end reads in samtools / pysam
... Pierre Lindenbaum did suggest this in a comment above. Did you try it? Is it fast, and does it get all reads (assuming they're a proper pair, non-duplicate, etc.)? It may be worth the overhead of sorting by query name. ...
written 2.2 years ago by olavur100

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Popular Question 15 months ago, created a question with more than 1,000 views. For Iterating through paired-end reads in samtools / pysam
Popular Question 15 months ago, created a question with more than 1,000 views. For Call missing variants in VCF as reference allele
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: How to add trio information to VCF or PED format (to compute Mendel error in Pli
Popular Question 18 months ago, created a question with more than 1,000 views. For How to add trio information to VCF or PED format (to compute Mendel error in Plink)
Popular Question 18 months ago, created a question with more than 1,000 views. For How to add trio information to VCF or PED format (to compute Mendel error in Plink)
Popular Question 20 months ago, created a question with more than 1,000 views. For How to add trio information to VCF or PED format (to compute Mendel error in Plink)
Popular Question 20 months ago, created a question with more than 1,000 views. For How to add trio information to VCF or PED format (to compute Mendel error in Plink)
Popular Question 22 months ago, created a question with more than 1,000 views. For How to add trio information to VCF or PED format (to compute Mendel error in Plink)
Popular Question 23 months ago, created a question with more than 1,000 views. For Samtools gives "truncated file" when trying to view a "reheaded" file
Popular Question 2.2 years ago, created a question with more than 1,000 views. For How to add trio information to VCF or PED format (to compute Mendel error in Plink)
Popular Question 2.5 years ago, created a question with more than 1,000 views. For How to add trio information to VCF or PED format (to compute Mendel error in Plink)
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