verifybamId for GRCH38 reference

[Lavi Bharath]

Hi,

I am trying to use verifyBamID (version 1.1.3) for GRCh38 reference. 

 verifyBamID --vcf GRCh38.sites.vcf.gz --bam WHH2871.bqsr.cram --out test --noPhoneHome --precise --maxDepth 100 --minMapQ 20 --minQ 20 --maxQ 100

As reference has "chr" as prefix, I liftover my vcf to GRCh38 reference and added "chr" as prefix.

But I still get the following warning and results are not getting generated by verifyBamID with 

the following warning and generated no meaningful results

WARNING : Cannot find sequence name chr1 appeared in VCF file but not in the BAM file, perhaps the reference is incompatible?
These markers will be ignored..
WARNING : Cannot find sequence name chr2 appeared in VCF file but not in the BAM file, perhaps the reference is incompatible?
These markers will be ignored..

cat test.selfRG 

#SEQ_ID RG CHIP_ID #SNPS #READS AVG_DP FREEMIX FREELK1 FREELK0  FREE_RH FREE_RA CHIPMIX CHIPLK1 CHIPLK0 CHIP_RH CHIP_RA DPREF   RDPHET  RDPALT

cram file header as below

@HD     VN:1.5  SO:coordinate
@SQ     SN:chr1 LN:248956422
@SQ     SN:chr2 LN:242193529
@SQ     SN:chr3 LN:198295559
@SQ     SN:chr4 LN:190214555
@SQ     SN:chr5 LN:181538259
@SQ     SN:chr6 LN:170805979
@SQ     SN:chr7 LN:159345973
@SQ     SN:chr8 LN:145138636
@SQ     SN:chr9 LN:138394717

vcf header as follows:

##fileformat=VCFv4.1
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##contig=<ID=chr1,assembly=GRCh37,length=249250621>
##contig=<ID=chr2,assembly=GRCh37,length=243199373>
##contig=<ID=chr3,assembly=GRCh37,length=198022430>
##contig=<ID=chr4,assembly=GRCh37,length=191154276>
##contig=<ID=chr5,assembly=GRCh37,length=180915260>
##contig=<ID=chr6,assembly=GRCh37,length=171115067>
##contig=<ID=chr7,assembly=GRCh37,length=159138663>
##contig=<ID=chr8,assembly=GRCh37,length=146364022>
##contig=<ID=chr9,assembly=GRCh37,length=141213431>

Could you please let me know whether I am missing anything here

 

[kiran girdhar]

Why does your vcf file has grch37 instead of grch38?

and what is the ref file in bam file?

KG

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[Lavi Bharath]

Sorry, header was wrongly added here. I have converted (picard liftover) vcf to grch38 build.

When I tried using bam instead of cram, verifybam is completed successfully.

So this tool can take only bam as the input file? And cram support is not available? Thanks.

KG

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