Hello to all,
I have 10 vcf files - 5 female fish and 5 male fish, I have merged all 10 fish to one vcf file.(all_fish.vcf) I performed the VcfSampleCompare analysis on 'all_fish.vcf' ,
following this:https://github.com/hepcat72/vcfSampleCompare
The example command :
vcfSampleCompare.pl --sample-group 'wt1 wt2 wt3' --sample-group 'mut1 mut2 mut3' input.vcf
The values used must match the vcf file headers for those samples (appearing after the 'FORMAT' column header). Each list is space-delimited and each group must be wrapped in quotes.
My command:
F1 F2 F4 F6 F8 is female fish M1 M3 M5 M7 M9 is male fish...
And this is my all_fish.vcf:
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT /storage/users/IsanaRNA/FISH_DATA/MappingToAcipenserRuthenusGenome/results/Bam_sorted/M1.sorted.bam.gz /storage/users/IsanaRNA/FISH_DATA/MappingToAcipenserRuthenusGenome/results/Bam_sorted/M3.sorted.bam.gz /storage/users/IsanaRNA/FISH_DATA/MappingToAcipenserRuthenusGenome/results/Bam_sorted/M5.sorted.bam.gz /storage/users/IsanaRNA/FISH_DATA/MappingToAcipenserRuthenusGenome/results/Bam_sorted/M7.sorted.bam.gz/storage/users/IsanaRNA/FISH_DATA/MappingToAcipenserRuthenusGenome/results/Bam_sorted/M9.sorted.bam.gz /storage/users/IsanaRNA/FISH_DATA/MappingToAcipenserRuthenusGenome/results/Bam_sorted/F1.sorted.bam.gz /storage/users/IsanaRNA/FISH_DATA/MappingToAcipenserRuthenusGenome/results/Bam_sorted/F2.sorted.bam.gz /storage/users/IsanaRNA/FISH_DATA/MappingToAcipenserRuthenusGenome/results/Bam_sorted/F4.sorted.bam.gz /storage/users/IsanaRNA/FISH_DATA/MappingToAcipenserRuthenusGenome/results/Bam_sorted/F6.sorted.bam.gz /storage/users/IsanaRNA/FISH_DATA/MappingToAcipenserRuthenusGenome/results/Bam_sorted/F8.sorted.bam.gz
NC_048323.1 53 . C T 26.2715 . VDB=0.0249187;SGB=-0.511536;RPBZ=-1.41421;MQBZ=1.41421;BQBZ=1.41421;SCBZ=0.57735;FS=0;MQ0F=0;MQ=18;DP=4;DP4=1,0,3,0;AN=2;AC=2 GT:PL ./.:. ./.:. ./.:. ./.:. ./.:. 1/1:53,5,0 ./.:. ./.:. ./.:. ./.:. NC_048323.1 129 . C CA 28.7159 . INDEL;IDV=3;IMF=0.6;VDB=0.444886;SGB=-0.511536;RPBZ=0.57735;MQBZ=0.888523;FS=0;MQ0F=0.2;MQ=24;DP=5;DP4=2,0,3,0;AN=2;AC=1 GT:PL ./.:. 0/1:62,0,16 ./.:. ./.:. ./.:. ./.:../.:. ./.:. ./.:. ./.:. .....................
the output file:
vcfSampleCompare.pl Version 2.013
Directory:
/storage/users/IsanaRNA/FISH_DATA/MappingToAcipenserRuthenusGenome/vcfsamplecompare
Command: /home/nevosmic/.conda/envs/mic/bin/perl /home/nevosmic/.conda/envs/mic/bin/vcfSampleCompare.pl --sample-group "/storage/users/IsanaRNA/FISH_DATA/MappingToAcipenserRuthenusGenome/results/Bam_sorted/F1.sorted.bam.gz /storage/users/IsanaRNA/FISH_DATA/MappingToAcipenserRuthenusGenome/results/Bam_sorted/F2.sorted.bam.gz /storage/users/IsanaRNA/FISH_DATA/MappingToAcipenserRuthenusGenome/results/Bam_sorted/F4.sorted.bam.gz /storage/users/IsanaRNA/FISH_DATA/MappingToAcipenserRuthenusGenome/results/Bam_sorted/F6.sorted.bam.gz /storage/users/IsanaRNA/FISH_DATA/MappingToAcipenserRuthenusGenome/results/Bam_sorted/F8.sorted.bam.gz" --sample-group "/storage/users/IsanaRNA/FISH_DATA/MappingToAcipenserRuthenusGenome/results/Bam_sorted/M1.sorted.bam.gz /storage/users/IsanaRNA/FISH_DATA/MappingToAcipenserRuthenusGenome/results/Bam_sorted/M3.sorted.bam.gz /storage/users/IsanaRNA/FISH_DATA/MappingToAcipenserRuthenusGenome/results/Bam_sorted/M5.sorted.bam.gz /storage/users/IsanaRNA/FISH_DATA/MappingToAcipenserRuthenusGenome/results/Bam_sorted/M7.sorted.bam.gz /storage/users/IsanaRNA/FISH_DATA/MappingToAcipenserRuthenusGenome/results/Bam_sorted/M7.sorted.bam.gz" /storage/users/IsanaRNA/FISH_DATA/MappingToAcipenserRuthenusGenome/Merged_vcf/all_fish.vcf
CHROM POS ID REF ALT BEST_PAIR BEST_GT_SCORE BEST_OR_SCORE BEST_DP_SCORE PAIR_ID PAIR_GT_SCORE PAIR_OR_SCORE PAIR_DP_SCORE STATES_USED_GT STATES_USED_OR GROUP1_SAMPLES GROUP1_GTS GROUP1_ORS GROUP2_SAMPLES GROUP2_GTS GROUP2_ORS
error file:
WARNING1:vcfSampleCompare.pl: Runtime warning: [Use of uninitialized value $dp in numeric gt (>) at /home/nevosmic/.conda/envs/mic/bin/vcfSampleCompare.pl line 2149.]. WARNING2:vcfSampleCompare.pl: Runtime warning: [Use of uninitialized value $dp in addition (+) at /home/nevosmic/.conda/envs/mic/bin/vcfSampleCompare.pl line 2149.]. WARNING3:vcfSampleCompare.pl: Runtime warning: [Use of uninitialized value $dp in numeric gt (>) at /home/nevosmic/.conda/envs/mic/bin/vcfSampleCompare.pl line 2149.]. WARNING3:vcfSampleCompare.pl: NOTE: Further warnings of this type will be suppressed. WARNING3:vcfSampleCompare.pl: Set --error-limit to 0 to turn off error suppression WARNING11:vcfSampleCompare.pl: Runtime warning: [Use of uninitialized value $dp in numeric gt (>) at /home/nevosmic/.conda/envs/mic/bin/vcfSampleCompare.pl line 2154.]. WARNING12:vcfSampleCompare.pl: Runtime warning: [Use of uninitialized value $dp in addition (+) at /home/nevosmic/.conda/envs/mic/bin/vcfSampleCompare.pl line 2154.]. WARNING13:vcfSampleCompare.pl: Runtime warning: [Use of uninitialized value $dp in numeric gt (>) at /home/nevosmic/.conda/envs/mic/bin/vcfSampleCompare.pl line 2154.]. WARNING13:vcfSampleCompare.pl: NOTE: Further warnings of this type will be suppressed. WARNING13:vcfSampleCompare.pl: Set --error-limit to 0 to turn off error suppression
Done. STATUS: [EXIT-CODE: 0 ERRORS: 0 WARNINGS: 1487319520 TIME: 71590s] SUMMARY: 743659760 WARNINGS LIKE: [WARNING1:vcfSampleCompare.pl: Runtime warning: [Use of uninitialized value $dp in numeric gt (>) at ...] 743659760 WARNINGS LIKE: [WARNING11:vcfSampleCompare.pl: Runtime warning: [Use of uninitialized value $dp in numeric gt (>) at...] Scroll up to inspect full errors/warnings in-place.
