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Did not get a summary of callable base counts
I am Calling SNPs using Unified Genotyper. I am using the Version GATK 2.5.2.
java -Djava.io.tmpdir=TMP -jar /GenomeAnalysisTK/2.5.2/GenomeAnalysisTK.jar -R Ref.fa -T UnifiedGenotyper -I input1.bam -I input2.bam -I input3.bam -o output.raw.vcf -stand_call_conf 50 -stand_emit_conf 20 -out_mode EMIT_ALL_CONFIDENT_SITES.
Usually I get A summary of callable base counts: Like
INFO 00:23:29,795 UnifiedGenotyper - Visited bases 247249719 INFO 00:23:29,796 UnifiedGenotyper - Callable bases 219998386 INFO 00:23:29,796 UnifiedGenotyper - Confidently called bases 219936125 INFO 00:23:29,796 UnifiedGenotyper - % callable bases of all loci 88.978 INFO 00:23:29,797 UnifiedGenotyper - % confidently called bases of all loci 88.953 INFO 00:23:29,797 UnifiedGenotyper - % confidently called bases of callable loci 88.953 INFO 00:23:29,797 UnifiedGenotyper - Actual calls made 303126
But I did not get it. Can you tell me how can I calculate this from my output VCF file now?