Moderator: Jorge Amigo
Jorge Amigo ♦ 9.8k
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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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C: Filter Bam File Based On Coverage
... first, you have to detect those low coverage regions. then, you have to filter your bam file with those regions. I would suggest you open a new question rather than commenting a previous related one. ...
written 16 days ago by
Jorge Amigo ♦ 9.8k
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... in addition, if you have already plotted depths it means that you have got a temporal R data.frame (or similar type) in there containing chromosome, position and depth information. splitting such data.frame by chromosome and calculating average values should be straight-forward. I would just suggest ...
written 12 weeks ago by
Jorge Amigo ♦ 9.8k
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... it seems to be a problem with my `java` calling script. I also use aliases for `java7` and `java8`, although I didn't include them in the original question. it works fine when calling java directly and not through the aliases, so I'll have to correct my aliases for the future. thanks anyway ;)
by t ...
written 4 months ago by
Jorge Amigo ♦ 9.8k
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... I tried both escaping and not escaping the quotes with no success. I even found out that the `gatkFlags` option even accepts a string (well, a single word) even without being quoted. but nothing gets recognized after the first word. ...
written 4 months ago by
Jorge Amigo ♦ 9.8k
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... I've run it both from a script and manually, both with single and double quotation marks, both using a variable $THREADS and a fixed value. no success.
I've edited the second example, since it was a copy-paste problem. I first tried using the large '--num_threads' option and then I also tried the ...
written 4 months ago by
Jorge Amigo ♦ 9.8k
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... I have this issue: when I try to test `RNA-SeQC` using GATK's multi-threading I'm not seeing the entire `gatkFlags` string being read:
java -jar $HOME/ngs/software/RNA-SeQC_v1.1.8.jar \
-strictMode \
-o $RNASEQC_FOLDER \
-r $REFERENCE_FASTA \
-t $REFERENCE_TRANSCRIPTOMIC \
- ...
written 4 months ago by
Jorge Amigo ♦ 9.8k
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3
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3
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... you're right. I didn't realize the `-m 1` option that stops reading the file after the first match. ...
written 5 months ago by
Jorge Amigo ♦ 9.8k
0
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2
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... in case you need to perform this 2-step process, it'd be much faster first to filter by region and then to select the samples. anyway, you can merge both commands in one:
bcftools view -r 3:38589548-38691164 -S list_of_Punjabi_persons.txt -o PJL_SCN5A.vcf 1000_genomes_chr3.vcf ...
written 5 months ago by
Jorge Amigo ♦ 9.8k
2
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4
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1.3k
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4
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... already stated [here][1] and [here][2]:
for file in *.vcf*; do
for sample in `bcftools query -l $file`; do
bcftools view -c1 -Oz -s $sample -o ${file/.vcf*/.$sample.vcf.gz} $file
done
done
[1]: https://www.biostars.org/p/78929/#115693
[2]: https://www.biostars.org/ ...
written 6 months ago by
Jorge Amigo ♦ 9.8k
0
votes
5
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848
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5
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... already stated [here][1] and [here][2]:
for file in *.vcf*; do
for sample in `bcftools query -l $file`; do
bcftools view -c1 -Oz -s $sample -o ${file/.vcf*/.$sample.vcf.gz} $file
done
done
[1]: https://www.biostars.org/p/78929/#115693
[2]: https://www.biostars.org/ ...
written 6 months ago by
Jorge Amigo ♦ 9.8k
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For A: Filtration of bam file but with header
Teacher
8 weeks ago,
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For A: Which Version Of Gatk Do People Use
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For A: Which Version Of Gatk Do People Use
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For A: Building Vcftools Executable
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For Which Programs Are You Relying On For Solid Data Analysis?
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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 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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