Question: chr20 length problem
gravatar for waqasnayab
4.4 years ago by
waqasnayab200 wrote:


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 / 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 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.

contig length reference gatk • 1.7k views
ADD COMMENTlink written 4.4 years ago by waqasnayab200

Hello waqasnayab!

It appears that your post has been cross-posted to another site:

This is typically not recommended as it runs the risk of annoying people in both communities.

ADD REPLYlink written 4.4 years ago by Pierre Lindenbaum126k

It would help if you posted the actual command that you issued. My guess is that you just specified a wrong file somewhere.

ADD REPLYlink written 4.4 years ago by Devon Ryan94k
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