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Picard GenotypeConcordance was over in the middle of chr2.

Hi,

I am using Picard GenotypeConcordance.
I tried to compare two vcf files. I could get the result, but it was halfway.
The command was 'java -jar picard.jar GenotypeConcordance \TRUTH_VCF=PG2572_01_b.vcf \TRUTH_SAMPLE=PG2572_01_b \CALL_VCF=PG3149_01_a.vcf \CALL_SAMPLE=PG3149_01_a \O=PG3149_01_a_PG257201_b \OUTPUT_VCF=true'.

And the command line was,

INFO 2019-04-11 18:41:44 GenotypeConcordance Starting iteration over variants.
INFO 2019-04-11 18:41:45 GenotypeConcordance checked 10,000 variants. Elapsed time: 00:00:01s. Time for last 10,000: 0s. Last read position: chr1:4,736,774
~~~~~~~(omission)~~~~~~~~~
INFO 2019-04-11 18:42:02 GenotypeConcordance checked 680,000 variants. Elapsed time: 00:00:18s. Time for last 10,000: 0s. Last read position: chr2:165,005,044

It was over here, in the middle of chr2.
Both vcf files have the full date.

What happened and how can I resolve?

I do appreciate your help.

Best Regards.

Answers

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