Sortie 12 : comparasion avec un vt peek entre une detection avec un fixMisencodedQuals et un allowMisencodedQuals - Dioufamad/SNPs_Calling GitHub Wiki
[adiouf@node21 test8_3_1_HaplotypeCaller]$ vt peek AX227_vsMSU7_bwamem_pp_nodup_sorted_idxed_realignedbam_raw_snp_indels.vcf.gz peek v0.5
options: input VCF file AX227_vsMSU7_bwamem_pp_nodup_sorted_idxed_realignedbam_raw_snp_indels.vcf.gz
stats: no. of samples : 1 no. of chromosomes : 16
========== Micro variants ==========
no. of SNP : 416106
2 alleles : 416096 (2.51) [297661/118435]
3 alleles : 10 (0.54) [7/13]
no. of INDEL : 42733
2 alleles : 42733 (0.84) [19557/23176]
no. of SNP/INDEL : 1
3 alleles : 1 (0.00) [0/1] (0.00) [0/1]
no. of micro variants : 458840
++++++ Other useful categories +++++
no. of complex substitutions : 1
3 alleles : 1 (0.00) [0/1] (0.00) [0/1]
========= General summary ==========
no. of VCF records : 458840
Time elapsed: 2.39s
[adiouf@node21 test8_3_1_HaplotypeCaller]$ vt peek AX227_vsMSU7_bwamem_pp_nodup_sorted_idxed_realignedbam_misencBQSallowed_raw_snp_indels.vcf.gz peek v0.5
options: input VCF file AX227_vsMSU7_bwamem_pp_nodup_sorted_idxed_realignedbam_misencBQSallowed_raw_snp_indels.vcf.gz
stats: no. of samples : 1 no. of chromosomes : 16
========== Micro variants ==========
no. of SNP : 426052
2 alleles : 426042 (2.51) [304559/121483]
3 alleles : 10 (0.54) [7/13]
no. of INDEL : 41412
2 alleles : 41412 (0.84) [18923/22489]
no. of SNP/INDEL : 1
3 alleles : 1 (0.00) [0/1] (0.00) [0/1]
no. of micro variants : 467465
++++++ Other useful categories +++++
no. of complex substitutions : 1
3 alleles : 1 (0.00) [0/1] (0.00) [0/1]
========= General summary ==========
no. of VCF records : 467465
Time elapsed: 2.45s
[adiouf@node21 test8_3_1_HaplotypeCaller]$