User: emmanouil.a

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emmanouil.a10
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Posts by emmanouil.a

<prev • 8 results • page 1 of 1 • next >
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split vcf, choice
... 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 ...
vcf mergedvcf spltvcf written 7 months ago by emmanouil.a10
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(Closed) Qsub + job array + while read; do; done
... 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 - ...
job array while read do done qsub sge written 9 months ago by emmanouil.a10
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Comment: A: GATK4 training for beginners
... Hi Keniv, thank you. You can close this post. Thank you very much! ...
written 10 months ago by emmanouil.a10
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GATK4 training for beginners
... 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 ...
gatk4 training written 10 months ago by emmanouil.a10 • updated 8 months ago by vdauwera890
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Comment: C: an alternative "join" option for annotated-vcf handling in trios
... many thanks! I will try and I let you know ^_* ...
written 10 months ago by emmanouil.a10
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Comment: C: an alternative "join" option for annotated-vcf handling in trios
... just using the sort command sort sample1 > FILE1 ...
written 10 months ago by emmanouil.a10
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Comment: C: an alternative "join" option for annotated-vcf handling in trios
... 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 10 months ago by emmanouil.a10
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an alternative "join" option for annotated-vcf handling in trios
... 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_ ...
trio vcf written 10 months ago by emmanouil.a10 • updated 10 months ago by Pierre Lindenbaum115k

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