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brentp / smoove

structural variant calling and genotyping with existing tools, but, smoothly.
Apache License 2.0
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Why REF = N? #228

Open robertzeibich opened 10 months ago

robertzeibich commented 10 months ago

Do you know why for the REF N is displayed? Is there also a way to obtain the ALT sequence?

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT GALF003

chr1 789502 440 N 87.49 . SVTYPE=DUP;SVLEN=223225049;END=224014551;STRANDS=-+:9;IMPRECISE;CIPOS=-407,29;CIEND=-30,342;CIPOS95=-100,7;CIEND95=-9,72;SU=9;PE=9;SR=0;PRPOS=3.61176e-16,4.1447e-16,4.74956e-16,5.44 769e-16,6.24786e-16,7.14135e-16,8.18997e-16,9.37485e-16,1.07223e-15,1.23006e-15,1.40581e-15,1.60444e-15,1.83034e-15,2.0893e-15,2.38585e-15,2.73204e-15,3.11754e-15,3.55584e-15,4.07309e-15,4.66368e-15,5.30318e-15,6.04938e-15,6.89666e-15,7. 84477e-15,8.9712e-15,1.02639e-14,1.16718e-14,1.33188e-14,1.51842e-14,1.73273e-14,1.97681e-14,2.24816e-14,2.56338e-14,2.92283e-14,3.31236e-14,3.76362e-14,4.27849e-14,4.87925e-14,5.54265e-14,6.29927e-14,7.17939e-14,8.16114e-14,9.29521e-14, 1.05538e-13,1.19858e-13,1.3633e-13,1.54996e-13,1.7624e-13,2.00383e-13,2.27962e-13,2.58967e-13,2.94094e-13,3.34295e-13,3.79576e-13,4.30449e-13,4.88936e-13,5.54634e-13,6.28493e-13,7.12433e-13,8.06341e-13,9.14775e-13,1.03816e-12,1.17942e-12 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-14,1.94111e-14,1.68357e-14,1.47332e-14,1.28086e-14,1.11338e-14;AC=1;AN=2 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/1:6:87.49:-9,-1,-1:43:33:9:33:9:0:0:0:33:9:0.21

pingxinxing commented 4 weeks ago

Has this problem been solved? Whether my file is merged or VCF file after genotyping with --genotype, the column of REF is "N".