lofreq vcfplot issues

[Ge-Wu-pir]

Hi,
I have been having these error/Traceback messages after running lofreq vcfplot. Just wondering if anyone has come across this before and how should I fix this? Thank you very much.

Regards,
Ge

[andreas-wilm]

That is indeed strange. Something is going wrong in matplotlib's violinplot routine. Without sharing the vcf it's near impossible to tell what's going on. You might have to plot manually. Or if you have write access tp lofreq2_vcfplot.py you could comment out line 533

[Ge-Wu-pir]

Hi Andres,

Thank you very much for your speedy reply.
here is the content of one of my vcf files. Could you please provide more insights on this issue please?

##fileformat=VCFv4.0
##fileDate=20230830
##source=lofreq call -f /mnt/lustre/RDS-ephemeral/wu/clinical_pirbright/11E_1/D388_DeNoAln_consMOG_S_only.fa --no-default-filter -r D388_DeNoAln_consMOG_S_only:1-238 -o /tmp/lofreq2_call_parallelI3EK1R/0.vcf.gz /mnt/lustre/RDS-ephemeral/wu/clinical_pirbright_2/7D1/7D1.sorted.map.bam
##reference=/mnt/lustre/RDS-ephemeral/wu/clinical_pirbright/11E_1/D388_DeNoAln_consMOG_S_only.fa
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">
##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
##FILTER=<ID=min_snvqual_45,Description="Minimum SNV Quality (Phred) 45">
##FILTER=<ID=min_indelqual_20,Description="Minimum Indel Quality (Phred) 20">
##FILTER=<ID=min_dp_10,Description="Minimum Coverage 10">
##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
##FILTER=<ID=min_snvqual_59,Description="Minimum SNV Quality (Phred) 59">
##FILTER=<ID=min_indelqual_20,Description="Minimum Indel Quality (Phred) 20">
##FILTER=<ID=min_af_0.010000,Description="Minimum allele frequency 0.010000">
##FILTER=<ID=min_dp_1000,Description="Minimum Coverage 1000">
##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
#CHROM POS ID REF ALT QUAL FILTER INFO
D388_DeNoAln_consMOG_S_only 142 . G T 80 PASS DP=1306;AF=0.012251;SB=0;DP4=1284,0,16,0
D388_DeNoAln_consMOG_S_only 154 . G T 302 PASS DP=1306;AF=0.031394;SB=0;DP4=1261,0,41,0
D388_DeNoAln_consMOG_S_only 208 . G T 168 PASS DP=2231;AF=0.011206;SB=27;DP4=1278,925,22,3
D388_DeNoAln_consMOG_S_only 2022 . G T 130 PASS DP=1476;AF=0.013550;SB=0;DP4=1453,0,20,0
D388_DeNoAln_consMOG_S_only 2052 . G T 60 PASS DP=1477;AF=0.014218;SB=0;DP4=1452,2,21,0
D388_DeNoAln_consMOG_S_only 2406 . A G 97 PASS DP=6238;AF=0.011542;SB=134;DP4=2422,3738,60,12
D388_DeNoAln_consMOG_S_only 2408 . A T 189 PASS DP=6239;AF=0.017791;SB=59;DP4=2451,3671,20,91
D388_DeNoAln_consMOG_S_only 2553 . C A 272 PASS DP=4044;AF=0.012117;SB=1;DP4=97,3894,0,49
D388_DeNoAln_consMOG_S_only 2913 . G T 63 PASS DP=1582;AF=0.012010;SB=2;DP4=1475,85,19,0

Many thanks,
Ge