Moderator: Jorge Amigo
Jorge Amigo ♦ 12k
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- Santiago de Compostela, Spain
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- 10 years, 5 months ago
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Scrutinizing genomic human variation by dealing with high throughput genotyping and next generation sequencing results, among many other things.
Posts by Jorge Amigo
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Comment:
C: Merge coordinates by gene ID
... I really like the rationale behind using the 4th column as chromosome and keeping the chromosome as mapping information with `-c` option. I love finding different ways of using tools that were designed to do a particular job in order to achieve a different goal. ...
written 2 days ago by
Jorge Amigo ♦ 12k
3
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answer
52
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... From [bcftools' documentation][1]:
bcftools view -s HG00479 -o HG00479.chr9.vcf ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/ALL.chr9.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz
No ...
written 7 days ago by
Jorge Amigo ♦ 12k
1
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1
answer
147
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... I can think of simplifying the regex a little bit using perl, in case it helps:
perl -pe 's/\^\[\[(2J|3J|H|[01](;3[237])?m)//g; s/\^H//g; s/\|\/-//' run.log > run_clean.log ...
written 12 days ago by
Jorge Amigo ♦ 12k
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2
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... Assuming both read_count.csv and all genefamilies.csv are tabulated files containing 2 columns (read_count.csv doesn't really matter), and that ´awk´ number formatting is enough for you:
for file in *.genefamilies.csv; do
awk -v m=$(grep -F -w ${file/.genefamilies.csv} read_count.csv | awk ...
written 19 days ago by
Jorge Amigo ♦ 12k
0
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5
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... Without knowing what exactly have you done, I'll assume that you have copied the second piece of code of my answer into `splitvcf.pl` and ran it to split all 1000g samples, and you're seeing that error you describe. If that's the case, you've done one thing right and one thing wrong: the right thing ...
written 26 days ago by
Jorge Amigo ♦ 12k
0
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6
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Comment:
C: Splitting A Vcf File
... If `ALLsamples.vcf` is a well formed multisample file, and is previously `bgzip` compressed, `tabix -p vcf ALLsamples.vcf.gz` should index it without complaining at all. Unfortunately if that doesn't work for you you'll have to find it out yourself, as you're facing a local issue. Some ideas: is tab ...
written 27 days ago by
Jorge Amigo ♦ 12k
0
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6
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15k
views
6
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Comment:
C: Splitting A Vcf File
... Share the command you used with us, so that we don't have to guess it. ...
written 27 days ago by
Jorge Amigo ♦ 12k
0
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1
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169
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1
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... This is not a Python solution, but Perl, and it's meant to be run in a unix/linux command line. Also, the sequences.fa file is expected to have unix EOL, so if that's not the case you may have to preprocess it with dos2unix or mac2unix.
Also, this solution addresses exactly what your question was a ...
written 28 days ago by
Jorge Amigo ♦ 12k
2
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1
answer
169
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1
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... If a perl solution can be considered, here are my 2 cents:
perl -pe 'if (/^>/) { $. > 1 and print "\n" } else { chomp }' sequences.fa \
| perl -pe '/^(-*)\w+(-*)$/ and printf "%s %s\n", length($1), length($2)'
The first perl section linearizes the fasta file, and the second perl sect ...
written 29 days ago by
Jorge Amigo ♦ 12k
0
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Comment:
C: Linearize fasta files
... Wow, what a nice comparison. Unfortunately I must say that my perl suggestion doesn't work as expected:
$ time (perl -pe 'chomp unless /^>/' < Homo_sapiens.GRCh38.dna.primary_assembly.fa > /dev/null)
does indeed join each header to the end of the previous sequence. This very slightly ...
written 29 days ago by
Jorge Amigo ♦ 12k
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For A: Which Version Of Gatk Do People Use
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For A: Check if REF allele is minor allele in any variant
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For C: How To Analyse Snp Data From Different Sources?
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For A: Which Version Of Gatk Do People Use
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For A: Is It Ok To Use One End Of A Set Of Paired-End Reads As A Set Of Single Reads?
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For A: Is It Ok To Use One End Of A Set Of Paired-End Reads As A Set Of Single Reads?
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For A: Filtration of bam file but with header
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For A: Filtration of bam file but with header
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For A: Is It Ok To Use One End Of A Set Of Paired-End Reads As A Set Of Single Reads?
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