Hi,

I have an Abi SOLiD WGS csfasta reads. After QC and filtering steps, I aligned the reads via SHRiMP2, specific for csfasta reads. I used hg19 as reference downloaded from ftp://ftp.broadinstitute.org/bundle/2.8/hg19/. SAM file is converted to BAM to sorted BAM to markduplicates (remove duplicates false) to reordersam to validatesam by PICARD. Than, I used GATK for realignertargetcreator but I got the followed error:

ERROR MESSAGE: Input files known and reference have incompatible contigs: Found contigs with the same name but different lengths:
##### ERROR   contig known = chr20 / 6444167
##### ERROR   contig reference = chr20 / 63025520

I never ever changed or modified or touched the reference file (any sort of reference file whether it is ucsc.hg19.fasta or ucsc.hg19.dict or ucsc.hg19.fasta.fai). I checked files , such as, in BAM header or all reference files, the length of chr20 is reported as 63025520. I also checked --known files, 1000G_phase1.indels.hg19.sites.vcf and Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz

(which I downloaded from ftp://ftp.broadinstitute.org/bundle/2.8/hg19/) where the chr20 length is 63025520. I don't know from where the length of chr20 64444167 comes here? I religned again and again and got the same error.

Thanks in advance

Waqasuddin Khan.