User: bari.ballew
bari.ballew • 190
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Posts by bari.ballew
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... Try altering chr11_snp_pos.txt to have a single tab-delimited position per line, as described in the vcftools documentation. E.g.:
1195855385
1172496148
Are there two different alt alleles at position 11:72496148? That could result in more than one line for a single position in the VCF. ...
written 4 months ago by
bari.ballew • 190
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... FastQC names output files by taking the original filename, removing the `.fastq` extension, and replacing the extension with `_fastqc.html` or `_fastqc.zip`. So, your output should be `reports/{sample}.trimmed_fastq.html` and `reports/{sample}.trimmed_fastq.zip`
Also, you only need to include the ...
written 4 months ago by
bari.ballew • 190
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... What exactly is "Non-Tumor"? To call somatic variants in your tumor sample, you should use a somatic caller (e.g. MuTect2) with the blood sample as the normal. If Non-Tumor is a nearby normal, that is, a biopsy of normal tissue taken adjacent or very close to the site of the tumor, I would not rec ...
written 4 months ago by
bari.ballew • 190
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... Take a look at regex anchors, which tie your pattern to the beginning or end of a line. You can use sed to remove whitespace at the beginning of a line only using "^", which anchors the pattern to the beginning of the line.
sed 's/^[\t ]*//' file.fa > secondFile.fa
...
written 4 months ago by
bari.ballew • 190
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... To expand on what [RamRS][1] said, if you've merged VCFs and not gVCFs, note that VCFs only report a genomic location if there is a variant in that individual, so you are susceptible to a missing data problem. When a variant is reported in A.vcf, but not in B.vcf, the merged file will record the var ...
written 5 months ago by
bari.ballew • 190
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... You want to concatenate (add rows), not merge (add individuals). See my answer [here][1].
[1]: https://www.biostars.org/p/390264/#390538 ...
written 5 months ago by
bari.ballew • 190
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... You can get awk to behave differently for different rows by using conditional statements based on either line number:
(NR==1) {do something} (NR>1) {do something else}
Or by a characteristic of the line:
$0~/^#CHROM/ {do something} $0!~/^#CHROM/ {do something else}
HOWEVER, I strongly ...
written 5 months ago by
bari.ballew • 190
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... This question is rather old and has an accepted answer, but I'll add another option since [Ikirola](https://www.biostars.org/u/57233/) has found the post and is having trouble.
Try [bcftools isec](https://samtools.github.io/bcftools/bcftools.html#isec). Make a minimal sites-only vcf containing y ...
written 5 months ago by
bari.ballew • 190
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Answer:
A: VCF merge or concatenate?
... Take a look at `bcftools concat` (https://samtools.github.io/bcftools/bcftools.html#concat).
In general, concatenate means adding on rows to your vcf (e.g. re-combining split chromosomes), while merge means creating a superset of variant calls across multiple individuals. Concatenating is relati ...
written 6 months ago by
bari.ballew • 190
0
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... It sounds like MutSig2CV is looking for, but not finding, a gene name column called either "gene," "Hugo_Symbol," or "Gene_name." Can you show us the first few lines of your input file? ...
written 6 months ago by
bari.ballew • 190
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