updating rsids of 1000 genomes project vcf file with dbsnp1444

Question

[waqasnayab]

Hi,

I have only chr1 vcf file of 1000 genomes project. I want to update the column ID with rsids. I used the following command:

/home/lgiu/Desktop/usr/java/jdk1.7.0_79/bin/java \
  -Xmx16g \
  -Djava.io.tmpdir=java_tmp \
  -XX:MaxPermSize=512m \
  -XX:-UseGCOverheadLimit \
  -jar /home/lgiu/Desktop/snpEff/SnpSift.jar \
  annotate 00-All.vcf 1000_chr1.vcf > 1000_chr1_anntedbsnp144.vcf

I downloaded the 00-All.vcf file from ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b144_GRCh37p13/VCF/00-All.vcf.gz

The error is:

java.lang.RuntimeException: Cannot find 'Description' in info line: '##INFO=<ID=ACmle,Number=A,Type=Integer,Description="">'
    at ca.mcgill.mcb.pcingola.vcf.VcfHeaderInfo.<init>(VcfHeaderInfo.java:127)
    at ca.mcgill.mcb.pcingola.vcf.VcfHeaderEntry.factory(VcfHeaderEntry.java:17)
    at ca.mcgill.mcb.pcingola.vcf.VcfHeader.parseInfoLines(VcfHeader.java:412)
    at ca.mcgill.mcb.pcingola.vcf.VcfHeader.getVcfInfo(VcfHeader.java:236)
    at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdAnnotate.headers(SnpSiftCmdAnnotate.java:237)
    at ca.mcgill.mcb.pcingola.snpSift.SnpSift.addHeaders(SnpSift.java:86)
    at ca.mcgill.mcb.pcingola.snpSift.SnpSift.processVcfHeader(SnpSift.java:357)
    at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdAnnotate.annotate(SnpSiftCmdAnnotate.java:79)
    at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdAnnotate.run(SnpSiftCmdAnnotate.java:403)
    at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdAnnotate.run(SnpSiftCmdAnnotate.java:391)
    at ca.mcgill.mcb.pcingola.snpSift.SnpSift.run(SnpSift.java:372)
    at ca.mcgill.mcb.pcingola.snpSift.SnpSift.main(SnpSift.java:70)

Need help in this regard.

Thanks,
Waqas.

[GouthamAtla]

try using -id