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LoFreq Star: Sensitive variant calling from sequencing data
http://csb5.github.io/lofreq/
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lofreq vcfplot issues #135

Open Ge-Wu-pir opened 10 months ago

Ge-Wu-pir commented 10 months ago

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.

image

Regards, Ge

andreas-wilm commented 10 months ago

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 commented 10 months ago

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=

INFO=

INFO=

INFO=

INFO=

INFO=

INFO=

FILTER=

FILTER=

FILTER=

FILTER= 0.001000">

FILTER=

FILTER=

FILTER=

FILTER=

FILTER= 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