CombineGVCFs outputs genomic region out of specified intervals
I am using CombineGVCFs module to merge a number of individual WGS gVCFs generated by Haplotype caller into a single gVCF files. The -L argument was used to restrict processing on a specific genomic intervals chr1:100000001-150000000. However, the output gVCF file contains info from region chr1:99999813-100000000 which supposed to be excluded from output.
Did I make a mistake?
Here is my command-line:
gatk --java-options "-Xmx4G -XX:+PrintCommandLineFlags -XX:ParallelGCThreads=1" CombineGVCFs -R hg38.fa -L chr1:100000001-150000000 --variant gvcf.list -O combine50_1.chr1.100000001-150000000.g.vcf.gz