I want to use bedtools makewindows first to create a sliding window over the genome and later to compute GC content with bedtools nuc. However, I am having some issues with the makewindows tools, since the intervals seem not to correspond to what is being introduced in the options. For example:

bedtools makewindows -b file.vcf -w 1000 
bedtools makewindows -b file.vcf -w 1000 -s 1

Both generate a file with the first lines being like:

C0001   14      15
C0001   15      16
C0001   16      17
C0001   17      18

Consider also the following short VCF file for reproducibiliy:

##fileformat=VCFv4.2
C0001   15      .       G       .       0       .       DP=1;DPB=1;EPPR=5.18177;GTI=0;MQMR=33;NS=27;NUMALT=0;ODDS=0;PAIREDR=1;PQR=0;PRO=0;QR=65;RO=1;RPPR=5.18177       GT:DP:AD:RO:QR:AO:QA:GL .       .       .       .     ..       .       .       .       .       .       .       .       .       .       0:1:1:1:65:.:.:0        .       .       .       .       .       .       .       .       .       .       .
C0001   16      .       C       .       0       .       DP=1;DPB=1;EPPR=5.18177;GTI=0;MQMR=33;NS=27;NUMALT=0;ODDS=0;PAIREDR=1;PQR=0;PRO=0;QR=65;RO=1;RPPR=5.18177       GT:DP:AD:RO:QR:AO:QA:GL .       .       .       .     ..       .       .       .       .       .       .       .       .       .       0:1:1:1:65:.:.:0        .       .       .       .       .       .       .       .       .       .       .
C0001   17      .       T       .       0       .       DP=1;DPB=1;EPPR=5.18177;GTI=0;MQMR=33;NS=27;NUMALT=0;ODDS=0;PAIREDR=1;PQR=0;PRO=0;QR=65;RO=1;RPPR=5.18177       GT:DP:AD:RO:QR:AO:QA:GL .       .       .       .     ..       .       .       .       .       .       .       .       .       .       0:1:1:1:65:.:.:0        .       .       .       .       .       .       .       .       .       .       .
C0001   18      .       T       .       0       .       DP=1;DPB=1;EPPR=5.18177;GTI=0;MQMR=33;NS=27;NUMALT=0;ODDS=0;PAIREDR=1;PQR=0;PRO=0;QR=65;RO=1;RPPR=5.18177       GT:DP:AD:RO:QR:AO:QA:GL .       .       .       .     ..       .       .       .       .       .       .       .       .       .       0:1:1:1:65:.:.:0        .       .       .       .       .       .       .       .       .       .       .
C0001   19      .       G       .       0       .       DP=1;DPB=1;EPPR=5.18177;GTI=0;MQMR=33;NS=27;NUMALT=0;ODDS=0;PAIREDR=1;PQR=0;PRO=0;QR=65;RO=1;RPPR=5.18177       GT:DP:AD:RO:QR:AO:QA:GL .       .       .       .     ..       .       .       .       .       .       .       .       .       .       0:1:1:1:65:.:.:0        .       .       .       .       .       .       .       .       .       .       .
C0001   20      .       C       .       0       .       DP=1;DPB=1;EPPR=5.18177;GTI=0;MQMR=33;NS=27;NUMALT=0;ODDS=0;PAIREDR=1;PQR=0;PRO=0;QR=69;RO=1;RPPR=5.18177       GT:DP:AD:RO:QR:AO:QA:GL .       .       .       .     ..       .       .       .       .       .       .       .       .       .       0:1:1:1:69:.:.:0        .       .       .       .       .       .       .       .       .       .       .

Running bedtols makewindows -b file.vcf -w 2 -s 1 on it will generate again windows of size 1 and not 2. What is going on?