problem in annotate my vcf file with another vcf file ??

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7.7 years ago

rastogi.suraj93 ▴ 30

hello every one, I am trying to annotate my vcf files which is generate using same reference genome for both vcf files but query reads is different. after alignment and SNP calling i got vcf file and count also variants. now i want to annotate these files to each other. i am using vcf annotate command like this

cat input.vcf.gz | vcf-annotate -a input2.vcf.gz -d column=HASH[0x2],key=INFO,ID=INDEL,Number=0,type=flag,Description=my annotate files -c CHROM,POS,ID,REF,ALT | bgzip -c > output.vcf

this command is working and dont show any error at window but output result i am not getting proper as a vcf format.i appreciate if can some one tell me how to access this command proper and get good result?? Thanking you

SNP next-gen genome • 2.2k views

ADD COMMENT • link updated 7.5 years ago by Biostar 20 • written 7.7 years ago by rastogi.suraj93 ▴ 30

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"this command is working and showing error" ? Can you rephrase the question ?

ADD REPLY • link 7.7 years ago by GouthamAtla 12k

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sorry, I again edit my question...please check it

ADD REPLY • link 7.7 years ago by rastogi.suraj93 ▴ 30

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Should you not be using zcat input.vcf.gz with a gzipped file?

ADD REPLY • link 7.7 years ago by GenoMax 141k

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sorry, i used but i forgot to mention there ..

ADD REPLY • link 7.7 years ago by rastogi.suraj93 ▴ 30

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