No sample column

[kostasgalexiou]

Hi,

The following command is not giving me a sample column at the generated VCF. The VCF file stops at the INFO column.

/home/kalexiou/local/software/lofreq/src/lofreq/lofreq call \
--no-default-filter \
--ref /projects/133-IRTA_Genomas/tomato_genome/Solanum_lycopersicum/SL_4.0/S_lycopersicum_chromosomes.4.00.fa \
--out temp.vcf \
--bed ../../../pcr_products.bed \
-m 20 \
DpTOM10_S10_L001_filtered_sort_pcrCoords.RG.bam

LoFreq does detect SNP variants, as can be seen from the output below, but these do not appear in the vcf.

Number of substitution tests performed: 18711
Number of indel tests performed: 0

Thanks