Question about `bcftools merge` handling of ALT as '' in gVCF

[zx0223winner]

Dear bcftools maintainer,

I have a quick question about using bcftools merge. It turns out the bcftools could not recognize the ALT as '' in the gvcf file (yielded by Octopus) after merging. Those lines with '' was treated as missing (./.........) in the merged file. Please find an example here:

By looking at the merged gvcf, at location 55, the sample 13T1500006 was treated as missing, however if you check this individual below, it actually suggests from 53 to 71 are all homozygous 0/0 with DP = 8 , but bcftools treat it as missing. Here I used blocked gvcf due to the size efficiency, how to let bcftools not treat those blocked gvcf region as missing if DP (coverage) is high. I also tried -gvcf to vcf, it wound help a lot.

Melup_Chr1 53 . A * 10.47 AD;ADP AC=0;AN=2;DP=8;END=71;MQ=27;NS=1 GT
:GQ:DP:MQ:FT 0|0:15:8:27:AD,ADP

Will thank for your time looking into this.

this is merged vcf file (13T1500003, 13T1500006, 13T1500009)

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  13T1500003      13T1500006
13T1500009
Melup_Chr1      1       .       T       *       3       q10;MQ;AD;DP;ADP        END=54;MQ=0;NS=0;DP=8;
AN=6;AC=0       GT:GQ:DP:MQ:FT  0|0:3:0:0:q10,MQ,AD,DP,ADP      0|0:3:4:27:q10,AD,ADP   0|0:3:4:27:q10
,AD,ADP
Melup_Chr1      53      .       A       *       10.47   AD;ADP  END=71;MQ=27;NS=1;DP=8;AN=2;AC=0
GT:GQ:DP:MQ:FT  ./.:.:.:.:.     0|0:15:8:27:AD,ADP      ./.:.:.:.:.
Melup_Chr1      55      .       G       *       6.67    q10;AD;ADP      END=93;MQ=42;NS=1;DP=11;AN=2;A
C=0     GT:GQ:DP:MQ:FT  0|0:15:11:42:q10,AD,ADP ./.:.:.:.:.     ./.:.:.:.:.
Melup_Chr1      67      .       G       *       14.02   AD;ADP  END=162;MQ=27;NS=1;DP=7;AN=2;AC=0
GT:GQ:DP:MQ:FT  ./.:.:.:.:.     ./.:.:.:.:.     0|0:15:7:27:AD,ADP

this is an individual gvcf file (13T1500003)

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  13T1500003
Melup_Chr1      1       .       T       *       3       q10;MQ;AD;DP;ADP        AC=0;AN=2;DP=0;END=54;
MQ=0;NS=0       GT:GQ:DP:MQ:FT  0|0:3:0:0:q10,MQ,AD,DP,ADP
Melup_Chr1      55      .       G       *       6.67    q10;AD;ADP      AC=0;AN=2;DP=11;END=93;MQ=42;N
S=1     GT:GQ:DP:MQ:FT  0|0:15:11:42:q10,AD,ADP
Melup_Chr1      94      .       C       *       0.85    q10;AD;ADP      AC=0;AN=2;DP=14;END=205;MQ=39;
NS=1    GT:GQ:DP:MQ:FT  0|0:3:14:39:q10,AD,ADP
Melup_Chr1      206     .       C       *       15.17   AD;ADP  AC=0;AN=2;DP=7;END=233;MQ=39;NS=1     
GT:GQ:DP:MQ:FT  0|0:21:7:39:AD,ADP
Melup_Chr1      234     .       T       *       3       q10;AD;ADP      AC=0;AN=2;DP=10;END=1910;MQ=45
;NS=1   GT:GQ:DP:MQ:FT  0|0:9:10:45:q10,AD,ADP

this is an individual gvcf file (13T1500006)

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  13T1500006
Melup_Chr1      1       .       T       *       3       q10;AD;ADP      AC=0;AN=2;DP=4;END=52;MQ=27;NS=1  
        GT:GQ:DP:MQ:FT  0|0:3:4:27:q10,AD,ADP
Melup_Chr1      53      .       A       *       10.47   AD;ADP  AC=0;AN=2;DP=8;END=71;MQ=27;NS=1        GT
:GQ:DP:MQ:FT    0|0:15:8:27:AD,ADP
Melup_Chr1      72      .       G       *       22.13   AD;ADP  AC=0;AN=2;DP=11;END=88;MQ=27;NS=1       GT
:GQ:DP:MQ:FT    0|0:27:11:27:AD,ADP
Melup_Chr1      89      .       A       *       1.38    q10     AC=0;AN=2;DP=11;MQ=27;NS=1      GT:GQ:DP:M
Q:FT    0|0:1:11:27:q10