about extract fq form hg38 with alt contig or hg38 without alt contig

[LI-DINGYANG]

Regarding the alignment of fq to hg38 with alt contig and hg38 without alt contig, the size of fq.gz extracted by specHLA is very different (for the same sample). The size of fq extracted from bam of hg38 with alt contig is more than 100 megabytes, while the size of fq extracted from bam of hg38 without alt contig is more than 10 megabytes. Is this reasonable? Is it true that the fq extracted from bam of hg38 with alt contig will be better in theory?

[wshuai294]

It is kind of weired with such a significant fq file size difference. Could you please check the typing results' consistency between these two fq files?