Question: If I have a .vcf file, how can I convert it to .bam file?

Answer: **EDIT**: found that one in **GATK3** https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_simulatereads_SimulateReadsForVariants.php ( now https://github.com/broadgsa/gatk-protected/blob/master/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariants.java )

>Given a set of variants, this tool will generate simulated reads that support the input variants.

I wrote an experimental tool to create a BAM from a VCF: http://lindenb.github.io/jvarkit/VcfToBam.html

$ java -jar dist/vcf2bam.jar -R ref.fa samtools.vcf.gz 2> /dev/null | grep -v "100="

@HD VN:1.5 SO:unsorted
@SQ SN:seg1 LN:5101
@SQ SN:seg2 LN:4000
@RG ID:NA12878 SM:NA12878 LB:illumina DS:NA12878
@RG ID:NA12891 SM:NA12891 LB:illumina DS:NA12891
@RG ID:NA12892 SM:NA12892 LB:illumina DS:NA12892
@CO Generated with -R /home/lindenb/src/ngsxml/test/ref/ref.fa /home/lindenb/src/ngsxml/OUT/Projects/Proj1/VCF/samtools/Proj1.samtools.vcf.gz
0000003609 83 seg1 1449 60 99=1X = 949 -500 TGCTTTAGAAAGCATTCCAAAATCTCTTACCAGTTTTATCTCCTATGAAAGTCCTTCACACTTTCTCTCATTTAAACTTTATTGCATTTTCCTCACTTTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:NA12891 NM:i:1
0000003610 147 seg1 1449 60 99=1X = 949 -500 TGCTTTAGAAAGCATTCCAAAATCTCTTACCAGTTTTATCTCCTATGAAAGTCCTTCACACTTTCTCTCATTTAAACTTTATTGCATTTTCCTCACTTTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:NA12891 NM:i:1
0000003611 147 seg1 1449 60 99=1X = 949 -500 TGCTTTAGAAAGCATTCCAAAATCTCTTACCAGTTTTATCTCCTATGAAAGTCCTTCACACTTTCTCTCATTTAAACTTTATTGCATTTTCCTCACTTTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:NA12892 NM:i:1
0000003612 83 seg1 1449 60 99=1X = 949 -500 TGCTTTAGAAAGCATTCCAAAATCTCTTACCAGTTTTATCTCCTATGAAAGTCCTTCACACTTTCTCTCATTTAAACTTTATTGCATTTTCCTCACTTTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:NA12892 NM:i:1
0000003615 83 seg1 1450 60 98=1X1= = 950 -500 GCTTTAGAAAGCATTCCAAAATCTCTTACCAGTTTTATCTCCTATGAAAGTCCTTCACACTTTCTCTCATTTAAACTTTATTGCATTTTCCTCACTTTCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:NA12891 NM:i:1
0000003616 147 seg1 1450 60 98=1X1= = 950 -500 GCTTTAGAAAGCATTCCAAAATCTCTTACCAGTTTTATCTCCTATGAAAGTCCTTCACACTTTCTCTCATTTAAACTTTATTGCATTTTCCTCACTTTCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:NA12891 NM:i:1
0000003617 147 seg1 1450 60 98=1X1= = 950 -500 GCTTTAGAAAGCATTCCAAAATCTCTTACCAGTTTTATCTCCTATGAAAGTCCTTCACACTTTCTCTCATTTAAACTTTATTGCATTTTCCTCACTTTCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:NA12892 NM:i:1
0000003627 147 seg1 1452 60 96=1X3= = 952 -500 TTTAGAAAGCATTCCAAAATCTCTTACCAGTTTTATCTCCTATGAAAGTCCTTCACACTTTCTCTCATTTAAACTTTATTGCATTTTCCTCACTTTCTCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:NA12891 NM:i:1
0000003629 147 seg1 1452 60 96=1X3= = 952 -500 TTTAGAAAGCATTCCAAAATCTCTTACCAGTTTTATCTCCTATGAAAGTCCTTCACACTTTCTCTCATTTAAACTTTATTGCATTTTCCTCACTTTCTCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:NA12892 NM:i:1
0000003630 147 seg1 1452 60 96=1X3= = 952 -500 TTTAGAAAGCATTCCAAAATCTCTTACCAGTTTTATCTCCTATGAAAGTCCTTCACACTTTCTCTCATTTAAACTTTATTGCATTTTCCTCACTTTCTCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:NA12892 NM:i:1
0000003633 147 seg1 1453 60 95=1X4= = 953 -500 TTAGAAAGCATTCCAAAATCTCTTACCAGTTTTATCTCCTATGAAAGTCCTTCACACTTTCTCTCATTTAAACTTTATTGCATTTTCCTCACTTTCTCTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:NA12891 NM:i:1
0000003635 83 seg1 1453 60 95=1X4= = 953 -500 TTAGAAAGCATTCCAAAATCTCTTACCAGTTTTATCTCCTATGAAAGTCCTTCACACTTTCTCTCATTTAAACTTTATTGCATTTTCCTCACTTTCTCTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:NA12892 NM:i:1
0000003640 147 seg1 1454 60 94=1X5= = 954 -500 TAGAAAGCATTCCAAAATCTCTTACCAGTTTTATCTCCTATGAAAGTCCTTCACACTTTCTCTCATTTAAACTTTATTGCATTTTCCTCACTTTCTCTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII RG:Z:NA12891 NM:i:1