Problem with Select Variant and Variant Filtration

Muriel_GBMuriel_GB Univ. Fribourg, SwitzerlandMember

Hello,

I obtained a vcf file using HaplotypeCaller.
Now I want to filter using SelectVariant and VariantFiltration.

java -Xmx20g -jar GenomeAnalysisTK.jar -T SelectVariants -R x.fasta -V input.vcf -L 20 -selectType SNP -o vcf_snp.vcf > vcf_snp.out

However, this is not working, it stops at one point and the reason why is not detailed :

...
514318212|gb|KE340275.1|, gi|514318211|gb|KE340276.1|, gi|514318210|gb|KE340277.1|, gi|514318209|gb|KE340278.1|, gi|514318208|gb|KE340279.1|, gi|514318207|gb|KE340280.1|, gi|514318206|gb|KE340281.1|, gi|514318205|gb|KE340282.1|, gi|514318204|gb|KE340283.1|, gi|514318203|gb|KE340284.1|, gi|514318202|gb|KE340285.1|, gi|514318201|gb|KE340286.1|, gi|514318200|gb|KE340287.1|, gi|514318199|gb|KE340288.1|, gi|514318198|gb|KE340289.1|, gi|514318197|gb|KE340290.1|, gi|514318196|gb|KE340291.1|, gi|514318195|gb|KE340292.1|, gi|514318194|gb|KE340293.1|, gi|514318193|gb|KE340294.1|, gi|514318192|gb|KE340295.1|, gi|514318191|gb|KE340296.1|]

ERROR ---------------------------------

The input vcf is a sample given that variant calling is still in progress and I just copied the vcf file in a new directory to work on it and 60% of the variant calling is done for this file.
Is it the reason why it's not working ?
Thanks a lot,

Muriel

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