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from gatk calling multiplesamples vcf to plink
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