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warning when running HaplotypeCaller

zzqzzq ChinaMember

Hi everyone,

I got the following warning when running the HaplotypeCaller.

BAM index file M11.bai is older than BAM M11.bam

Although the warning presents in the log, it also gives me a gvcf. Does this warning effect the accuracy of the result? I hope this warning will be fine for me.

I declare those bam files were produced on another server.

The command
java -Xmx50g -Djava.io.tmpdir=/data/tmp -jar /bin/GATK3.5/GenomeAnalysisTK.jar \ -R ref.fa \ -T HaplotypeCaller -nct 8 \ -I ./$d'.bam' \ -o $d'.g.vcf' \ --genotyping_mode DISCOVERY \ -stand_emit_conf 30 \ -stand_call_conf 30 \ -ERC GVCF done

What is more, I have another unsure on the new version highlights.

When I run above command with parameters -variant_index_type LINEAR -variant_index_parameter 128000, Do they will come to the same results?

Many thanks!

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