'just asking for confirmation: if I run IndelRealigner with option
-L my.capture.bed does indelrealigner:
i have SNPs from another SNP caller which does not produce vcf files so i wanted to convert those using the VariantsToVCF walker. I used the following command:
java -Xmx2g -jar /PATH/TO/GenomeAnalysisTK.jar -T VariantsToVCF -R reference.fa -o mySNPs.vcf --variant mySNPs.bed
GATK version 2.7-4
i took a bed file as input which had the following format:
chr1 895 896 chr1 941 942 chr1 1096 1097 ...
The walker runs without any error message but i get an empty vcf file (0B, nothing) apart from a mySNPs.vcf.idx and a mySNPs.bed.idx file.
Any idea how to fix that?
Thanks a lot!!!
Best wishes, Karin