User: emmanouil.a
emmanouil.a • 10
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Posts by emmanouil.a
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... Hi,
I have to split a multisample VCF (the output of GATK4) into single vcfs (per sample). What is the best code? Then I have to annotate them with AnnovaR.
vcf-subset -c samplename -e inputvcf > sample.vcf
bcftools view -Oz -s samplename inputvcf > sample.vcf.gz
Is it correct to ...
written 4 months ago by
emmanouil.a • 10
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... Hi!
just some help...
I'm using a "Sun Grid Engine" with "qsub"
In one hand I have this code
while read -r H; do echo ${H}; done < list
The number of the lines in the list file is 100.
On the other hand I want to create a job array with the option -t
echo "echo $H" | qsub -N loop - ...
written 6 months ago by
emmanouil.a • 10
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Comment:
A: GATK4 training for beginners
... Hi Keniv, thank you.
You can close this post.
Thank you very much! ...
written 7 months ago by
emmanouil.a • 10
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... Hi,
I'm a researcher in Italy and I'm looking for a research center in Europe that I can be a host for a short training on GATK4.
I'm new in GATK and I'm building the pipeline on Bash. For now I don't have access to a server where I can use the ready-to-use GATK4 WDL pipeline.
Please let me know ...
written 7 months ago by
emmanouil.a • 10
• updated
6 months ago by
vdauwera • 810
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... many thanks! I will try and I let you know ^_* ...
written 7 months ago by
emmanouil.a • 10
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... just using the sort command
sort sample1 > FILE1 ...
written 7 months ago by
emmanouil.a • 10
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... I sorted my files according to the first column (chr_start_end_ref_alt)... and some times the script works well and other time no... :-/
Ok, I will try with gatk and I will let you know, thank! ...
written 7 months ago by
emmanouil.a • 10
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... Server Linux, Bash 4.2.25
Hi,
I'm using this code to handle annotated-vcf files in trios:
join -t "`echo -e "\t"`" -e ND -a1 FILE1 FILE2 > OUTPUT
example:
FILE1 (space = tab)
chr1_11086439_11086439_C_T aaa,asf
chr1_11086717_11086717_A_G dad,ada
chr1_11087524_11087524_G_ ...
written 7 months ago by
emmanouil.a • 10
• updated
7 months ago by
Pierre Lindenbaum ♦ 112k
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