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Created 2015-01-26 20:35:50 | Updated | Tags: indelrealigner bed
Comments (1)

'just asking for confirmation: if I run IndelRealigner with option -L my.capture.bed does indelrealigner:

  • keep all the reads but only realign them in region of the bed ?
  • or only keep the reads in the given region (smaller BAM)?


Created 2013-12-04 09:21:16 | Updated 2013-12-04 22:09:48 | Tags: variantstovcf codec bed
Comments (6)


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