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from gatk calling multiplesamples vcf to plink

flrois_Bflrois_B GermanyMember
edited June 2014 in Ask the GATK team

Hi GATK team,

This is maybe a bit of a stupid question and I might not get the concept of calling samples at the same time. Anyway when I use this command for GATK for my 5 rnaseq samples to call SNPs:

java -jar /home//Desktop/variant_calling_rnaseq/GATK/GenomeAnalysisTK-3.1-1/GenomeAnalysisTK.jar \
   -R /media/Data/HG19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa \
   -T HaplotypeCaller \
   -I split1.bam -I split2.bam -I split3.bam -I split4.bam -I split5.bam\
   -o region_of_interest.vcf \
   --dbsnp /media/Data/HG19/Homo_sapiens/UCSC/hg19/Annotation/dbsnp141/new_all_141.vcf \
 -L chr1:30000000-38000000 \
   -stand_call_conf 50.0 \
   -stand_emit_conf 10.0 \
   -U ALLOW_N_CIGAR_READS

then I want to convert the vcf file to a plink file to continue analysis, then only one sample is present, while the input into GATK was 5 files:

$ vcftools --vcf region_of_interest.vcf --plink --out plink_file

VCFtools - v0.1.7
(C) Adam Auton 2009

Parameters as interpreted:
    --vcf region_of_interest.vcf
    --out plink_file
    --plink

VCF index is older than VCF file. Will regenerate.
Building new index file.
    Scanning Chromosome: chr1
Writing Index file.
File contains 46 entries and 1 individuals.
Applying Required Filters.
After filtering, kept 1 out of 1 Individuals
After filtering, kept 46 out of a possible 46 Sites
Writing PLINK PED file ... 
Writing PLINK MAP file ... Done.
Run Time = 0.00 seconds

Hope you can clarify this for me

Thanks, Floris

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