Moderator: finswimmer
finswimmer ♦ 11k
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Posts by finswimmer
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... For me this does not sound surprisingly.
If you have no sample within 1200 samples, which is hom REF on a given position, this means, that what is called ref, is very rare. Of course this is possible, but I would guess it is rare. ...
written 13 hours ago by
finswimmer ♦ 11k
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... Hmm, yes might be.
In this case:
bcftools view -e 'GT[*]="RR"' input.vcf ...
written 14 hours ago by
finswimmer ♦ 11k
1
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... I strongly recommend using existing tools for filtering vcf files.
With bcftools it works like this:
bcftools view -i 'GT[*]="alt"' input.vcf
This will give you any site where at least one sample has an alternate allel. ...
written 15 hours ago by
finswimmer ♦ 11k
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Comment:
C: -C 50 parameter MPILEUP
... Hello,
using this parameter `bcftools` penalize read with lot of mismatches harder than most aligner will do, which greatly improve specificity in variant calling. The thought behind this, is to say the more mismatches in one read exists the higher the probability that the origin of this read is in ...
written 1 day ago by
finswimmer ♦ 11k
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64
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Comment:
C: Custom filteration of fastq file
... > Remove reads with unique sequence having read count less than 10.
Could you please explain why do you want to do this? ...
written 1 day ago by
finswimmer ♦ 11k
1
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92
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Comment:
C: Error in SAM to BAM conversion
... Hello ,
./bowtie2 -p 5 -x /ref/grch38 --no-unal -U fastq/SRR7541164.fastq > -S /fastq/test.sam
Just a typo here or do you realy redirecte bowtie output to `-S`?
What's the output of `tail /fastq/test.sam`?
fin swimmer ...
written 2 days ago by
finswimmer ♦ 11k
2
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1
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52
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... > WARNING: Unkown IUB code for SNP '-'
You have a `-` in the 4th column (ALT) which is not allowed. Missing values have to be `.` in the vcf file.
Furthermore a chromosome `0` and a position `0` looks also quite strange (but should be allowed) ... ...
written 3 days ago by
finswimmer ♦ 11k
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72
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... Have a look if IGV filter out any reads. Go to View->Preferences->Alignment
Here the Mapping Quality Threshold and all point with "Filter" are the most interesting once. ...
written 5 days ago by
finswimmer ♦ 11k
2
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2
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94
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... Hello,
using the `--help` parameter or start bioinformatic applications without any option first is always a good idea.
$ tabix
Version: 1.9
Usage: tabix [OPTIONS] [FILE] [REGION [...]]
Indexing Options:
-0, --zero-based coordinates are zero-based
-b, --b ...
written 5 days ago by
finswimmer ♦ 11k
0
votes
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73
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0
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Comment:
C: snpEff for bacteria genome
... Hello,
what's the name of your bacteria? How does your `snpEff.config` looks like? Is `database` just a placeholder here?
fin swimmer ...
written 5 days ago by
finswimmer ♦ 11k
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