I am working on gwas data and ran bwa, GATK pipeline and generated vcf file of all the samples. After merging the vcf file using picard
java -jar /680_info4/project/arora/program/picard.jar MergeVcfs I=/680_info4/project/arora1/raw_variants.vcf I=/680_info4/project/arora2/raw_variants.vcf I=/680_info4/project/arora3/raw_variants.vcf I=/680_info4/project/arora4/raw_variants.vcf I=/680_info4/project/arora5/raw_variants.vcf I=/680_info4/project/arora6/raw_variants.vcf I=/680_info4/project/arora7/raw_variants.vcf O=all_raw_variant.vcf
When I ran pca plot script in plink it ran with an error saying only one sample and when I saw the same in vcf file and we have only one sample in merge file:
> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 20 >1 112 . C T 61.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.243;DP=117;ExcessHet=3.0103;FS=4.760;MLEAC=1;MLEAF=0.500;MQ=47.51;MQRankSum=-0.497;QD=0.5 3;ReadPosRankSum=-0.030;SOR=1.493 GT:AD:DP:GQ:PL 0/1:106,10:116:69:69,0,3944 >1 131 . G T 1457.60 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.046;DP=89;ExcessHet=3.0103;FS=2.787;MLEAC=1;MLEAF=0.500;MQ=49.38;MQRankSum=-0.647;QD=16. 38;ReadPosRankSum=-0.950;SOR=0.799 GT:AD:DP:GQ:PL 0/1:47,42:89:99:1465,0,1643
May I know what I an doing wrong? Any other way to merge vcf file or any suggestion are most welcome.