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Old 09-26-2015, 03:18 AM   #1
Waqasuddin Khan
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Location: Karachi

Join Date: Nov 2013
Posts: 7
Default chr20 length problem

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 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 / 64444167
##### 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 where the chr20 length is 63025520. I donít 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.
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Old 09-26-2015, 06:18 AM   #2
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Location: France

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cross posted
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Old 09-26-2015, 08:27 AM   #3
Richard Finney
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Location: bethesda

Join Date: Feb 2009
Posts: 700

grep chr20 chrom.sizes.hg*

chrom.sizes.hg18:chr20 62435964
chrom.sizes.hg19:chr20 63025520
chrom.sizes.hg38:chr20 64444167
Richard Finney is offline   Reply With Quote

chr20 contig length, gatk, reference

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