problem with vcf file by gatk
1
0
Entering edit mode
22 months ago
evelyn ▴ 140

Hello,

I am making vcf files using gatk with following codes:

java -jar $PICARD_DIR/picard.jar ValidateSamFile \
I=example.sorted.bam \
MODE=SUMMARY
java -jar $PICARD_DIR/picard.jar AddOrReplaceReadGroups \
I=example.sorted.bam \
O=example.gatk.sorted.bam \
RGID=1 \
RGLB=lib1 \
RGPL=illumina \
RGPU=unit1 \
RGSM=20
java -jar $PICARD_DIR/picard.jar ValidateSamFile \
I=example.gatk.sorted.bam \
MODE=SUMMARY
samtools index example.gatk.sorted.bam
gatk --java-options "-Xmx4G" HaplotypeCaller -R ref.fa -I example.gatk.sorted.bam -O example.gatk.vcf

But the vcf it gives does not give sample name in header line instead it gives a number 20 which I am not sure why:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  20

I want the sample name instead of 20 because I want to use the vcf files for further analysis where I am getting an error of duplicate names as all the vcf files have 20 instead of sample names.

I will appreciate any help. Thank you!

snp • 409 views
ADD COMMENT
4
Entering edit mode
22 months ago
Satyajeet Khare ★ 1.6k

You are declaring sample name to be 20 (RGSM=20).

ADD COMMENT

Login before adding your answer.

Traffic: 1787 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6