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4.1 years ago
elcortegano
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200
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?
