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file size - Haplotypecaller input file - > correlation with output *.g.vcf file
I have been making several g.vcf-files by Haplotpecaller, for later combined variantcalling. Usually there has been a reasonable correlation between the input recal*.bam file and the output g.vcf file. Like 81Gb (bam) -> 69 Gb (g.vcf), 101Gb (bam) -> 79 Gb (g.vcf). The last file I made - the biggest input-bam file I had so far (171 Gb) ended up, after maaaaanw hours With a g.vcf of just 27Gb.
Should I be worried- does the smaller file size indicate that somthing is wrong? (no special error Messages shown)