Problems with QV after merge

[BeaSamma]

Hi @fritzsedlazeck, I'm using SURVIVOR to merge the vcf outputs of 20 individuals. Each vcfs contains the SVs called by 5 different SVs caller (breackdancer, CNVnator, Manta, DELLY and Lumpy). Observing in detailed the QV for each individuals in the first mentioned vcf I noticed that in some cases I don't have a single QV but I have two of them (separed by ","). I report the here the header, the info of the format field and the lines in which I found this.

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 4051 4187 4212 4567 4573 4586 8391 8440 8657 8807 8811 8816 U1897 U1899 U1902 U1916 U1919 U1920 U1923 U1925
#GT:PSV:LN:DR:ST:QV:TY:ID:RAL:AAL:CO

grep -v "#" all_sample_merged.vcf | cut -f10 | cut -f6 -d: | grep -n ","
1001:305,59
1168:194,239
7466:257,413
14255:292,200
16671:198,158
20451:470,584
24476:644,602
28292:215,366

I'd like to produce some QV distribution to understand well how to filter my VCF. Do you have any suggestions on which value I should consider? One of the two values? Both or other?

Thanks for any suggestions,
Beatrice