Use of uninitialized value

[Giuseppe1995]

Hi,
I am trying to run the perl script svParse.pl on a structural variant vcf (normal-tumor) generated with Lumpy and genotyped with svTyper.
I want to apply the filters that you suggested to filter in somatic variants as follows:

perl $PERLDIR/svParse.pl \
-v $MYDIR/LumpyDir/$SAMPLE/NBD99-smoove.genotyped.vcf -f su=4 \     # min 4 reads supporting event in tumour
-f dp=10 \    # min read depth of 10 in both tumour/normal
-f rdr=0.1 \  # min 10% of reads at breakpoint supporting variant
-f sq=10 \    # min Log10 likelihood of 10
-f chr=0      # filter out calls on chromosomes not in 'chroms.txt' // this is actually not set 

What I unluckily got is thousands of lines of error messages with this pattern:

Use of uninitialized value $t_SR in numeric eq (==) at /srv/ngs/analysis/dalteriog/Tools/svParser/script/../bin/svParser.pm line 191, <$_[...]> line 11737.
(this is one of the last, but it happens for every field).

here I print the first 5 lines (along with the header) of my vcf
cat $MYDIR/LumpyDir/$SAMPLE/NBD99-smoove.genotyped.vcf | head -146

##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20220519
##reference=/srv/ngs/analysis/aievola/references/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/hs37d5.fa
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">
##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
##INFO=<ID=CIPOS95,Number=2,Type=Integer,Description="Confidence interval (95%) around POS for imprecise variants">
##INFO=<ID=CIEND95,Number=2,Type=Integer,Description="Confidence interval (95%) around END for imprecise variants">
##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">
##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
##INFO=<ID=SECONDARY,Number=0,Type=Flag,Description="Secondary breakend in a multi-line variants">
##INFO=<ID=SU,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples">
##INFO=<ID=PE,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples">
##INFO=<ID=SR,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples">
##INFO=<ID=BD,Number=.,Type=Integer,Description="Amount of BED evidence supporting the variant across all samples">
##INFO=<ID=EV,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call">
##INFO=<ID=PRPOS,Number=.,Type=String,Description="LUMPY probability curve of the POS breakend">
##INFO=<ID=PREND,Number=.,Type=String,Description="LUMPY probability curve of the END breakend">
##ALT=<ID=DEL,Description="Deletion">
##ALT=<ID=DUP,Description="Duplication">
##ALT=<ID=INV,Description="Inversion">
##ALT=<ID=DUP:TANDEM,Description="Tandem duplication">
##ALT=<ID=INS,Description="Insertion of novel sequence">
##ALT=<ID=CNV,Description="Copy number variable region">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">
##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant">
##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant">
##FORMAT=<ID=BD,Number=1,Type=Integer,Description="Amount of BED evidence supporting the variant">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
##FORMAT=<ID=SQ,Number=1,Type=Float,Description="Phred-scaled probability that this site is variant (non-reference in this sample">
##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally">
##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally">
##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of reference observations">
##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of alternate observations">
##FORMAT=<ID=RS,Number=1,Type=Integer,Description="Reference allele split-read observation count, with partial observations recorded fractionally">
##FORMAT=<ID=AS,Number=A,Type=Integer,Description="Alternate allele split-read observation count, with partial observations recorded fractionally">
##FORMAT=<ID=ASC,Number=A,Type=Integer,Description="Alternate allele clipped-read observation count, with partial observations recorded fractionally">
##FORMAT=<ID=RP,Number=1,Type=Integer,Description="Reference allele paired-end observation count, with partial observations recorded fractionally">
##FORMAT=<ID=AP,Number=A,Type=Integer,Description="Alternate allele paired-end observation count, with partial observations recorded fractionally">
##FORMAT=<ID=AB,Number=A,Type=Float,Description="Allele balance, fraction of observations from alternate allele, QA/(QR+QA)">
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##contig=<ID=3,length=198022430>
##contig=<ID=4,length=191154276>
##contig=<ID=5,length=180915260>
##contig=<ID=6,length=171115067>
##contig=<ID=7,length=159138663>
##contig=<ID=8,length=146364022>
##contig=<ID=9,length=141213431>
##contig=<ID=10,length=135534747>
##contig=<ID=11,length=135006516>
##contig=<ID=12,length=133851895>
##contig=<ID=13,length=115169878>
##contig=<ID=14,length=107349540>
##contig=<ID=15,length=102531392>
##contig=<ID=16,length=90354753>
##contig=<ID=17,length=81195210>
##contig=<ID=18,length=78077248>
##contig=<ID=19,length=59128983>
##contig=<ID=20,length=63025520>
##contig=<ID=21,length=48129895>
##contig=<ID=22,length=51304566>
##contig=<ID=X,length=155270560>
##contig=<ID=Y,length=59373566>
##contig=<ID=MT,length=16569>
##contig=<ID=GL000207.1,length=4262>
##contig=<ID=GL000226.1,length=15008>
##contig=<ID=GL000229.1,length=19913>
##contig=<ID=GL000231.1,length=27386>
##contig=<ID=GL000210.1,length=27682>
##contig=<ID=GL000239.1,length=33824>
##contig=<ID=GL000235.1,length=34474>
##contig=<ID=GL000201.1,length=36148>
##contig=<ID=GL000247.1,length=36422>
##contig=<ID=GL000245.1,length=36651>
##contig=<ID=GL000197.1,length=37175>
##contig=<ID=GL000203.1,length=37498>
##contig=<ID=GL000246.1,length=38154>
##contig=<ID=GL000249.1,length=38502>
##contig=<ID=GL000196.1,length=38914>
##contig=<ID=GL000248.1,length=39786>
##contig=<ID=GL000244.1,length=39929>
##contig=<ID=GL000238.1,length=39939>
##contig=<ID=GL000202.1,length=40103>
##contig=<ID=GL000234.1,length=40531>
##contig=<ID=GL000232.1,length=40652>
##contig=<ID=GL000206.1,length=41001>
##contig=<ID=GL000240.1,length=41933>
##contig=<ID=GL000236.1,length=41934>
##contig=<ID=GL000241.1,length=42152>
##contig=<ID=GL000243.1,length=43341>
##contig=<ID=GL000242.1,length=43523>
##contig=<ID=GL000230.1,length=43691>
##contig=<ID=GL000237.1,length=45867>
##contig=<ID=GL000233.1,length=45941>
##contig=<ID=GL000204.1,length=81310>
##contig=<ID=GL000198.1,length=90085>
##contig=<ID=GL000208.1,length=92689>
##contig=<ID=GL000191.1,length=106433>
##contig=<ID=GL000227.1,length=128374>
##contig=<ID=GL000228.1,length=129120>
##contig=<ID=GL000214.1,length=137718>
##contig=<ID=GL000221.1,length=155397>
##contig=<ID=GL000209.1,length=159169>
##contig=<ID=GL000218.1,length=161147>
##contig=<ID=GL000220.1,length=161802>
##contig=<ID=GL000213.1,length=164239>
##contig=<ID=GL000211.1,length=166566>
##contig=<ID=GL000199.1,length=169874>
##contig=<ID=GL000217.1,length=172149>
##contig=<ID=GL000216.1,length=172294>
##contig=<ID=GL000215.1,length=172545>
##contig=<ID=GL000205.1,length=174588>
##contig=<ID=GL000219.1,length=179198>
##contig=<ID=GL000224.1,length=179693>
##contig=<ID=GL000223.1,length=180455>
##contig=<ID=GL000195.1,length=182896>
##contig=<ID=GL000212.1,length=186858>
##contig=<ID=GL000222.1,length=186861>
##contig=<ID=GL000200.1,length=187035>
##contig=<ID=GL000193.1,length=189789>
##contig=<ID=GL000194.1,length=191469>
##contig=<ID=GL000225.1,length=211173>
##contig=<ID=GL000192.1,length=547496>
##contig=<ID=NC_007605,length=171823>
##contig=<ID=hs37d5,length=35477943>
##smoove_version=0.2.8
##smoove_count_stats=sample_control_XI003_NB-S_559:28112073,50782761,655708,915464
##smoove_count_stats=sample_tumor_XI003_NB-S_559:45240623,74879219,1439450,1092014
##source=LUMPY
##bcftools_viewVersion=1.15.1+htslib-1.15.1
##bcftools_viewCommand=view -O z -o NBD99-smoove.genotyped.vcf.gz; Date=Thu May 19 18:30:22 2022
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample_control_XI003_NB-S_559 sample_tumor_XI003_NB-S_559
1 10621 1 N 267.12 . SVTYPE=DEL;SVLEN=-132;END=10753;STRANDS=+-:8;CIPOS=-10,9;CIEND=-10,9;CIPOS95=0,0;CIEND95=0,0;SU=8;PE=0;SR=8;PRPOS=9.98739e-33,1.58289e-29,2.50872e-26,3.97605e-23,6.30162e-20,9.98739e-17,1.58289e-13,2.50872e-10,3.97605e-07,0.000630162,0.998739,0.000630162,3.97605e-07,2.50872e-10,1.58289e-13,9.98739e-17,6.30162e-20,3.97605e-23,2.50872e-26,1.58289e-29;PREND=9.98739e-33,1.58289e-29,2.50872e-26,3.97605e-23,6.30162e-20,9.98739e-17,1.58289e-13,2.50872e-10,3.97605e-07,0.000630162,0.998739,0.000630162,3.97605e-07,2.50872e-10,1.58289e-13,9.98739e-17,6.30162e-20,3.97605e-23,2.50872e-26,1.58289e-29 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 1/1:5:60.25:-6,-1,-0:2:0:2:0:2:0:2:0:0:0:1 1/1:17:206.87:-21,-2,-0:7:0:7:0:7:0:4:2:0:0:1
1 724849 441 N 1032.98 . SVTYPE=DUP;SVLEN=223477470;END=224202319;STRANDS=-+:35;IMPRECISE;CIPOS=-112,29;CIEND=-30,133;CIPOS95=-14,10;CIEND95=-11,21;SU=35;PE=35;SR=0;PRPOS=7.31826e-15,1.06072e-14,1.53884e-14,2.23119e-14,3.22149e-14,4.6432e-14,6.68358e-14,9.63105e-14,1.38067e-13,1.968e-13,2.80319e-13,3.98685e-13,5.65739e-13,8.00447e-13,1.13428e-12,1.59774e-12,2.24908e-12,3.15698e-12,4.44317e-12,6.2215e-12,8.71191e-12,1.21375e-11,1.68966e-11,2.34437e-11,3.25018e-11,4.48895e-11,6.19883e-11,8.55856e-11,1.17496e-10,1.61075e-10,2.19779e-10,3.00624e-10,4.0918e-10,5.56862e-10,7.56663e-10,1.02551e-09,1.38987e-09,1.87854e-09,2.53988e-09,3.42081e-09,4.59466e-09,6.17216e-09,8.25484e-09,1.10312e-08,1.47052e-08,1.96235e-08,2.60276e-08,3.45669e-08,4.58136e-08,6.0618e-08,7.98451e-08,1.0526e-07,1.38332e-07,1.81576e-07,2.37851e-07,3.11342e-07,4.07076e-07,5.30309e-07,6.90093e-07,8.96642e-07,1.16086e-06,1.5008e-06,1.94051e-06,2.50171e-06,3.22146e-06,4.14169e-06,5.3145e-06,6.82287e-06,8.73822e-06,1.11828e-05,1.42666e-05,1.81517e-05,2.3054e-05,2.92695e-05,3.71059e-05,4.69476e-05,5.94023e-05,7.49642e-05,9.4439e-05,0.000118739,0.000148988,0.000186701,0.000233416,0.000291159,0.000363116,0.000452758,0.000562259,0.000697707,0.000864503,0.00106861,0.0013195,0.00162918,0.00199927,0.00245865,0.00301755,0.00369195,0.00451476,0.00551105,0.00672747,0.00819528,0.00996772,0.0121071,0.0146637,0.0177225,0.0214036,0.0258517,0.0311365,0.0374675,0.0450298,0.0539719,0.0645381,0.0771325,0.0920682,0.0806902,0.0706603,0.0618243,0.0539144,0.0469061,0.0408498,0.0355114,0.0226553,0.0144417,0.00918749,0.00583393,0.00370107,0.0023405,0.00148176,0.000936035,0.000590878,0.000372162,0.000233828,0.000146939,9.20985e-05,4.24179e-05,1.95269e-05,4.85664e-06,1.20424e-06,2.98081e-07,7.37922e-08,1.8246e-08,4.50555e-09,1.11007e-09;PREND=7.77101e-11,4.50701e-10,2.60989e-09,1.11134e-08,4.7286e-08,2.01104e-07,8.54707e-07,2.67136e-06,8.33486e-06,1.91004e-05,4.37561e-05,0.000100151,0.000228848,0.000384975,0.000645942,0.00108297,0.00181478,0.00303932,0.00508236,0.00848684,0.0104301,0.0128009,0.0156758,0.0191859,0.0234613,0.0286814,0.0349932,0.042661,0.0519479,0.0632162,0.0768669,0.068606,0.0612592,0.0545988,0.0486238,0.043256,0.0384393,0.0341092,0.0302223,0.0267878,0.0237207,0.0209797,0.0185257,0.0163464,0.0143966,0.0126715,0.0111306,0.00977859,0.00858504,0.00752211,0.0065782,0.00574568,0.00501302,0.00437428,0.00381148,0.00331508,0.00287985,0.00249883,0.00216435,0.00187005,0.00161681,0.00139586,0.0012044,0.00103805,0.000893982,0.000767604,0.000658866,0.00056467,0.000483133,0.000413214,0.000352576,0.0003005,0.000255915,0.000217683,0.000184874,0.000156553,0.00013255,0.000111932,9.46469e-05,7.96953e-05,6.71155e-05,5.63835e-05,4.72711e-05,3.96004e-05,3.31596e-05,2.77039e-05,2.31293e-05,1.9246e-05,1.59975e-05,1.32687e-05,1.10127e-05,9.1263e-06,7.53889e-06,6.21187e-06,5.11649e-06,4.209e-06,3.45916e-06,2.83092e-06,2.31703e-06,1.89104e-06,1.54263e-06,1.25698e-06,1.02034e-06,8.27482e-07,6.70772e-07,5.42394e-07,4.37511e-07,3.52347e-07,2.83191e-07,2.27276e-07,1.81793e-07,1.45518e-07,1.15945e-07,9.24884e-08,7.3356e-08,5.82602e-08,4.61746e-08,3.64294e-08,2.87332e-08,2.25405e-08,1.77515e-08,1.39235e-08,1.0915e-08,8.54069e-09,6.67277e-09,5.18396e-09,4.02603e-09,3.1255e-09,2.41642e-09,1.86307e-09,1.43627e-09,1.10158e-09,8.45554e-10,6.45979e-10,4.92719e-10,3.7521e-10,2.854e-10,2.16169e-10,1.63226e-10,1.2322e-10,9.30143e-11,6.99968e-11,5.24524e-11,3.90691e-11,2.91149e-11,2.17142e-11,1.60905e-11,1.19055e-11,8.81017e-12,6.49288e-12,4.76735e-12,3.50126e-12,2.56285e-12,1.87162e-12,1.36617e-12,9.93474e-13,7.24336e-13,5.24877e-13,3.78815e-13,2.74174e-13,1.97486e-13,1.42036e-13,1.01795e-13,7.27046e-14 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 1/1:31:589.72:-60,-4,-1:151:100:51:100:50:62:0:6:38:44:0.33 1/1:26:443.27:-45,-4,-1:108:70:37:70:37:42:0:4:28:32:0.35
1 797367 7788_1 N N]8:245671] 32.57 . 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Can you tell me where is my mistake?
Thank you in advance,
Giuseppe