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VQSLOD score different for Full and split (by chromosome) BAM file

dasdevashishdasdasdevashishdas BangaloreMember

Dear all,

I am trying to generate VCF using full and split (by chromosome) BAM files by GATK but after successful completion, there are difference in the VQSLOD score:

For full : VQSLOD=-6.339e-01

For split : VQSLOD=-1.472e+00

Does this means splitting the BAM is not correct or is it because of wrong parameters? or it is correct and I can neglect this?

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