User: pd3
pd3 • 340
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Posts by pd3
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... 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
pd3 • 340
2
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1
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... 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
pd3 • 340
2
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4
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4
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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
pd3 • 340
0
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2
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2
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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
pd3 • 340
2
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6
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6
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... 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
pd3 • 340
0
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6
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... Can you please provide a sample of mpileup -uv output for testing?
...
written 5.1 years ago by
pd3 • 340
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... 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
pd3 • 340
0
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6
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14k
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6
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... 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
pd3 • 340
0
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6
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14k
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6
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... What happens if you drop -v? Could the simple explanation be that there are no non-reference calls?
...
written 5.2 years ago by
pd3 • 340
2
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3
answers
2.6k
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3
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... 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
pd3 • 340
Latest awards to pd3
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
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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