Below is some troubleshooting that reproduces the problem. They're not full-spec VCFs with the whole header, but they do isolate the problem. I finally narrowed it down: truncation only happens when there is a "##", followed by some text on the same line, and a blank line before the data.
Knowing this, I can now fix my files to get them to work, but I don't see anything in the VCF spec that disallows blank lines like that -- hence the bug report.
$ cat b.bed
chr10 3100000 3200000
a0.vcf original:
chr10 3127949 T A 46.3 . FQ=-28.7;DP4=0,0,4,1;AC1=6.0;VDB=0.08892796;MQ=20;AF1=1.0;DP=5 GT:PL:GQ 1/1:0,0,0:4 1/1:0,0,0:4 1/1:79,15,0:17
intersected:
chr10 3127949 T A 46.3 . FQ=-28.7;DP4=0,0,4,1;AC1=6.0;VDB=0.08892796;MQ=20;AF1=1.0;DP=5 GT:PL:GQ 1/1:0,0,0:4 1/1:0,0,0:4 1/1:79,15,0:17
a1.vcf original:
##fileformat=VCFv4.1
chr10 3127949 T A 46.3 . FQ=-28.7;DP4=0,0,4,1;AC1=6.0;VDB=0.08892796;MQ=20;AF1=1.0;DP=5 GT:PL:GQ 1/1:0,0,0:4 1/1:0,0,0:4 1/1:79,15,0:17
intersected:
chr10 3127949 T A 46.3 . FQ=-28.7;DP4=0,0,4,1;AC1=6.0;VDB=0.08892796;MQ=20;AF1=1.0;DP=5 GT:PL:GQ 1/1:0,0,0:4 1/1:0,0,0:4 1/1:79,15,0:17
a2.vcf original:
##fileformat=VCFv4.1
chr10 3127949 T A 46.3 . FQ=-28.7;DP4=0,0,4,1;AC1=6.0;VDB=0.08892796;MQ=20;AF1=1.0;DP=5 GT:PL:GQ 1/1:0,0,0:4 1/1:0,0,0:4 1/1:79,15,0:17
intersected:
chr10 3127949
a3.vcf original:
##
chr10 3127949 T A 46.3 . FQ=-28.7;DP4=0,0,4,1;AC1=6.0;VDB=0.08892796;MQ=20;AF1=1.0;DP=5 GT:PL:GQ 1/1:0,0,0:4 1/1:0,0,0:4 1/1:79,15,0:17
intersected:
chr10 3127949 T A 46.3 . FQ=-28.7;DP4=0,0,4,1;AC1=6.0;VDB=0.08892796;MQ=20;AF1=1.0;DP=5 GT:PL:GQ 1/1:0,0,0:4 1/1:0,0,0:4 1/1:79,15,0:17
a4.vcf original:
#comment
chr10 3127949 T A 46.3 . FQ=-28.7;DP4=0,0,4,1;AC1=6.0;VDB=0.08892796;MQ=20;AF1=1.0;DP=5 GT:PL:GQ 1/1:0,0,0:4 1/1:0,0,0:4 1/1:79,15,0:17
intersected:
chr10 3127949 T A 46.3 . FQ=-28.7;DP4=0,0,4,1;AC1=6.0;VDB=0.08892796;MQ=20;AF1=1.0;DP=5 GT:PL:GQ 1/1:0,0,0:4 1/1:0,0,0:4 1/1:79,15,0:17
a5.vcf original:
##fileformat=VCFv4.1
#CHROM
chr10 3127949 T A 46.3 . FQ=-28.7;DP4=0,0,4,1;AC1=6.0;VDB=0.08892796;MQ=20;AF1=1.0;DP=5 GT:PL:GQ 1/1:0,0,0:4 1/1:0,0,0:4 1/1:79,15,0:17
intersected:
chr10 3127949 T A 46.3 . FQ=-28.7;DP4=0,0,4,1;AC1=6.0;VDB=0.08892796;MQ=20;AF1=1.0;DP=5 GT:PL:GQ 1/1:0,0,0:4 1/1:0,0,0:4 1/1:79,15,0:17
a6.vcf original:
##fileformat=VCFv4.1
#CHROM
chr10 3127949 T A 46.3 . FQ=-28.7;DP4=0,0,4,1;AC1=6.0;VDB=0.08892796;MQ=20;AF1=1.0;DP=5 GT:PL:GQ 1/1:0,0,0:4 1/1:0,0,0:4 1/1:79,15,0:17
intersected:
chr10 3127949