Output vcf file: ALT is not sequence

[quentin0515]

Hi!

I'm using whamg by

export EXCLUDE=GL000207.1,GL000226.1,GL000229.1,GL000231.1,GL000210.1,GL000239.1,GL000235.1,GL000201.1,GL000247.1,GL000245.1,GL000197.1,GL000203.1,GL000246.1,GL000249.1,GL000196.1,GL000248.1,GL000244.1,GL000238.1,GL000202.1,GL000234.1,GL000232.1,GL000206.1,GL000240.1,GL000236.1,GL000241.1,GL000243.1,GL000242.1,GL000230.1,GL000237.1,GL000233.1,GL000204.1,GL000198.1,GL000208.1,GL000191.1,GL000227.1,GL000228.1,GL000214.1,GL000221.1,GL000209.1,GL000218.1,GL000220.1,GL000213.1,GL000211.1,GL000199.1,GL000217.1,GL000216.1,GL000215.1,GL000205.1,GL000219.1,GL000224.1,GL000223.1,GL000195.1,GL000212.1,GL000222.1,GL000200.1,GL000193.1,GL000194.1,GL000225.1,GL000192.1,NC_007605

whamg -e $EXCLUDE -r chr1:10000000-20000000 -a /reference/GRCh38_full_analysis_set_plus_decoy_hla.fa -f sample.bam | perl ./wham/utils/filtWhamG.pl > output.vcf 2> output.err

The result is like:

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096
chr1 948662 . C . PASS A=10;CIEND=-10,10;CIPOS=-10,10;CF=0;CW=0,1,0,0,0;D=0;DI=0;END=948730;EV=0;I=0;SR=10;SS=0;SVLEN=68;SVTYPE=DUP;T=0;TAGS=HG00096;TF=0;U=10;V=0 GT:DP:SP .:.:16

Instead of alt sequences, it gives sv type (). Is this as expected? Is it possible that I can get the alt sequences?
Many thanks!

[xiongzy1229]

I've run into the same issue. How did you resolve it in the end?