Open kostasgalexiou opened 2 years ago
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
/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
Number of substitution tests performed: 18711
Number of indel tests performed: 0
Thanks
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.bamLoFreq 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: 18711Number of indel tests performed: 0Thanks