Hey all.. I am currently trying to use LINKDATAGEN and facing a frequent problem mentioned by many users. My sample set is human and I performed exome sequencing using Hiseq2000. I generated BAM using Samtools/Picard. And for creating linkadatagen vcf, I used the following codes:
samtools mpileup -d10000 -q13 -Q13 -gf hg19.fa -l annotHapMap2U.txt samplex.bam | bcftools view -cg -t0.5 - > samplex.HM.vcf
Perl vcf2linkdatagen.pl -variantCaller mpileup -annotfile annotHapMap2U.txt -pop CEU -mindepth 10 -missingness 0 samplex.vcf > samplex.brlmm
The error I am getting is:
Use of uninitialized value $chr in concatenation (.) or string at vcf2linkdatagen.pl line 487, <IN> line 1.... to line 63964968
How to correct it? The same BAM file was used to generate vcf using GATK and it worked perfectly, so the parent file can't be the issue. It's just not working with this tool.
Any suggestion would be appreciated.
Thanks a lot
samtools mpileup -d10000 -q13 -Q13 -gf hg19.fa -l annotHapMap2U.txt samplex.bam | bcftools view -cg -t0.5 - > samplex.HM.vcf
Perl vcf2linkdatagen.pl -variantCaller mpileup -annotfile annotHapMap2U.txt -pop CEU -mindepth 10 -missingness 0 samplex.vcf > samplex.brlmm
The error I am getting is:
Use of uninitialized value $chr in concatenation (.) or string at vcf2linkdatagen.pl line 487, <IN> line 1.... to line 63964968
How to correct it? The same BAM file was used to generate vcf using GATK and it worked perfectly, so the parent file can't be the issue. It's just not working with this tool.
Any suggestion would be appreciated.
Thanks a lot