User: pd3

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pd3340
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Posts by pd3

<prev • 25 results • page 1 of 3 • next >
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Comment: C: bcftools consensus not working when using -H flag
... What version of bcftools are you running, can you try with the latest github version? I believe it should work, the tests in contain cases with missing genotypes. ...
written 12 months ago by pd3340
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Answer: A: Meaning of SGB field in samtools mpileup output
... Here are math notes for SGB calculation: http://samtools.github.io/bcftools/ http://samtools.github.io/bcftools/rd-SegBias.pdf ...
written 4.9 years ago by pd3340
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Answer: A: Query A Dbsnp Vcf File
... Try `bcftools view -i'%ID=@path/to/ids.txt' file.vcf` http://samtools.github.io/bcftools/bcftools.html ...
written 5.0 years ago by pd3340
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Answer: A: Find Rs# From Vcf
... Try `bcftools view -i'%ID=@path/to/ids.txt' file.vcf` http://samtools.github.io/bcftools/bcftools.html ...
written 5.0 years ago by pd3340
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Answer: A: Variant Calling With Bcftools Call
... There is not enough information to answer the original question, but Stephane's problem is caused by a version mismatch. Note that samtools and bcftools went through major changes, the new versions of bcftools will not work with pre-HTSlib versions of samtools. For the latest installation instructio ...
written 5.1 years ago by pd3340
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Comment: C: Variant Calling With Bcftools Call
... Can you please provide a sample of mpileup -uv output for testing? ...
written 5.1 years ago by pd3340
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Comment: C: Variant Calling With Bcftools Call
... I meant if you could run without bcftools at all like this: samtools mpileup -uv -f ref.fa -b sampleList | less. Are there any sites listed? If not, then there is something odd with your BAMs. Could all reads be excluded because of low quality for example? Is the result any different with -B,-x,-Q0? ...
written 5.1 years ago by pd3340
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Comment: C: Variant Calling With Bcftools Call
... This does not seem to be a samtools/htslib/bcftools compatibility problem, as you say you followed instructions from here http://samtools.github.io/bcftools/. If you run mpileup with -uv, it will produce raw VCF output. Are any sites listed? ...
written 5.1 years ago by pd3340
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Comment: C: Variant Calling With Bcftools Call
... What happens if you drop -v? Could the simple explanation be that there are no non-reference calls? ...
written 5.2 years ago by pd3340
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Answer: A: Are There Population-Specific Snps Included In The 1000Genomes Vcf Files?
... The VCFs contain population allele frequencies, AMR_AF, ASN_AF, AFR_AF, EUR_AF which can be used to filter sites more frequent in one population: bcftools view -i'EUR_AF > AMR_AF & EUR_AF > ASN_AF' file.vcf.gz (Link to bcftools.) ...
written 5.2 years ago by pd3340

Latest awards to pd3

Appreciated 4.8 years ago, created a post with more than 5 votes. For A: Dbsnp In Vcf
Appreciated 4.8 years ago, created a post with more than 5 votes. For A: Vdb Field In Samtools
Scholar 4.8 years ago, created an answer that has been accepted. For A: [Samtools] Dp4 Vs. Dp: Low-Quality Bases Not Counted
Teacher 4.8 years ago, created an answer with at least 3 up-votes. For A: [Samtools] Dp4 Vs. Dp: Low-Quality Bases Not Counted
Teacher 4.8 years ago, created an answer with at least 3 up-votes. For A: Dbsnp In Vcf
Teacher 5.1 years ago, created an answer with at least 3 up-votes. For A: Dbsnp In Vcf
Teacher 5.1 years ago, created an answer with at least 3 up-votes. For A: [Samtools] Dp4 Vs. Dp: Low-Quality Bases Not Counted

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