Moderator: Jorge Amigo
Jorge Amigo ♦ 11k
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Scrutinizing genomic human variation by dealing with high throughput genotyping and next generation sequencing results, among many other things.
Bioinformatician @ Genomic Medicine Group
Hospital Clínico Universitario, Santiago de Compostela, Spain
Posts by Jorge Amigo
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... sorting such a big file only for being able to use the uniq function wouldn't be the more efficient way to do it, plus a simple `sort -u` wouldn't address the problem described in the question as the lines that need to be merged/skipped do vary. if sorting would be considered (and it would be really ...
written 3 days ago by
Jorge Amigo ♦ 11k
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... this is the same as an uniq function on entire lines, and it doesn't work with your example considering that positions qualities vary from line to line. you need to group (index) only the columns you expect to be repeated, as explained in the example I suggested previously. ...
written 3 days ago by
Jorge Amigo ♦ 11k
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... I don't know of a direct method to accomplish what you need, but have a look at this tentative proposal:
awk 'FS=OFS="\t"{print $1, 0, $2}' human_hg19.fa.fai \
| bedtools makewindows -b - -w 1000 \
| bedtools map -a - -b input.bedgraph -c 4 -o sum \
| grep -P "\d$"
what it does is: ...
written 7 days ago by
Jorge Amigo ♦ 11k
2
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2
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79
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Comment:
C: awk gff column change
... not caring about the number of total columns:
awk '{n=split($1,a,"_"); $4+=a[n]; $5+=a[n]; print}' input.txt
not caring about the number of total columns, plus considering that both input and output are tabulated:
awk 'FS=OFS="\t"{n=split($1,a,"_"); $4+=a[n]; $5+=a[n]; print}' input.txt ...
written 7 days ago by
Jorge Amigo ♦ 11k
1
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181
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Answer:
A: filtering unique snps in vcf
... I don't fully understand why you want to do this, but if what you need is just to remove lines considered duplicated attending to certain columns, then this perl code should work:
perl -lane '
$index = join "\t", @F[0,7..$#F];
unless ( exists $found{$index} ) {
print; $found{$index ...
written 7 days ago by
Jorge Amigo ♦ 11k
1
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2
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79
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2
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Answer:
A: awk gff column change
... if the value you need to add to columns 4 and 5 is always behind a "_" character in the first column, then this perl code should work:
perl -lane 'if (/^\S+_(\d+)/) { $F[3] += $1; $F[4] += $1; print join "\t", @F}' input.txt ...
written 7 days ago by
Jorge Amigo ♦ 11k
1
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5
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20k
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5
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... the key is the `-c1`option, which filters variant lines containing less that 1 nonref allele, therefore it's supposed to be used to retrieve each sample's private variants and not to list reference homozigotes:
http://www.htslib.org/doc/bcftools.html#view
if you whish to have theses laters too in ...
written 5 weeks ago by
Jorge Amigo ♦ 11k
1
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3
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3.4k
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3
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... all mapped reads from r.sam would be that gene's reads.
# total reads
samtools view -c r.sam
# mapped reads
samtools view -cF4 r.sam
if you get a non 0 value from the -cF4 option, then those reads would be that gene's.
if you want to be sure that those reads are that gene's, and t ...
written 8 weeks ago by
Jorge Amigo ♦ 11k
1
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10
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47k
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10
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... thanks for pointing it out. I've corrected my previous answer and tested thoroughly the new one. ...
written 8 months ago by
Jorge Amigo ♦ 11k
1
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3
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11k
views
3
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... note that the merging process when normalizing can be quite intense on such large files as gnomad's, so if you are interested in particular regions do not forget to indicate this in your normalization command. I've edited my answer to reflect this. ...
written 9 months ago by
Jorge Amigo ♦ 11k
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