Moderator: finswimmer
finswimmer ♦ 13k
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Posts by finswimmer
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... Hello https://www.biostars.org/u/8531/,
could you please show some example lines of your vcf and the expected output?
Very likely [bcftools query](http://www.htslib.org/doc/bcftools.html#query) will help you with this task.
fin swimmer ...
written 3 days ago by
finswimmer ♦ 13k
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... Using [seqkit](https://bioinf.shenwei.me/seqkit/usage/#subseq):
$ seqkit subseq -r 1:30 input.fasta ...
written 3 days ago by
finswimmer ♦ 13k
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Comment:
C: Switch ref/alt alleles vcf file
... Hello mdstep,
if you have already a list of positions and REF/ALT alleles you want to switch, you could try something like this:
1. The list must be one of the support types by [bcftools annotate](http://www.htslib.org/doc/bcftools.html#annotate) and must contain an ID
2. Use this list and `bcftoo ...
written 7 days ago by
finswimmer ♦ 13k
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... Hey, try this:
$ bcftools query -l input.vcf | sort > samples.txt
$ bcftools view -S samples.txt input.vcf > output.vcf
If not already done, I would also suggest to use `bcf` instead of `vcf` or `vcf.gz`. This really improves speed when working with `bcftools` on large datasets.
fi ...
written 10 days ago by
finswimmer ♦ 13k
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... In this case `pysam` might be the right hammer ... :) ...
written 12 days ago by
finswimmer ♦ 13k
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Comment:
C: bcftools variant filteration
... Hello,
the `DP` value in the `INFO` is the sum of the DP value over all samples in your vcf at this position. The `DP` value in the `FORMAT` column in the read depth for the given sample at this position. If you just have one sample this value should be equal.
You have to decide which one you need ...
written 12 days ago by
finswimmer ♦ 13k
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... Hello,
could you please show the header and one variant line?
fin swimmer ...
written 18 days ago by
finswimmer ♦ 13k
1
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... Hello https://www.biostars.org/u/45196/ ,
you are mixing things up. BQSR (Base Quality Score Recalibration) and MarkDuplicates are two different things.
1 BQSR (Base Quality Score Recalibration):
The quality values assigned to each base within a read by sequencing machine gets reassigned by new v ...
written 21 days ago by
finswimmer ♦ 13k
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... The columns must be separated by whitespaces and not tabs. That's the only requirement.
> I get a syntax error.
When ever you receive any kind of error or something "doesn't work": Please give us the details!
fin swimmer ...
written 25 days ago by
finswimmer ♦ 13k
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... The warning is just a warning. You can ignore it for now or do what it suggest.
But there must be something strange with your input. I've tested it with the data you gave above and that's the output I get:
id SNP2 SNP3
162 BB AA
172 BB AB
189 BB AA
1590 AB BB
182 BB AA
...
written 25 days ago by
finswimmer ♦ 13k
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