Tom,
Thank you for your advice. CSI indexes worked fine at performing the
merge. TBI indexes from the merged file seem to load fine on JBrowse.
Cheers,
-Hans
On Tue, Aug 22, 2017 at 2:52 PM, Thomas W. Blackwell <tbla...@umich.edu>
wrote:
> Hans -
>
> Read the man page for 'bcftools index'. This has a brief description of
> the relative capabilities of .tbi versus .csi indexes. (.csi is bigger.)
> Sounds as though you are hitting the tabix limit of 2^29 - 1.
>
> - tom blackwell -
>
>
> On Tue, 22 Aug 2017, Hans Vasquez-Gross wrote:
>
> Hello,
>>
>> I am trying to merge 24 different individual sample VCF files (currently
>> testing with only 3 samples) into one large VCF file to display on JBrowse
>> as a single track. However, after merging the files, it seems like all the
>> data stops at around 536 Mbp per psuedomolecule.
>>
>> Below is an example single sample VCF ending for a particular chromosome,
>> and then the merged vcf output.
>>
>> Individual File:
>> zgrep "chr7A" G3116_CSv1_calls_full_chr_length.vcf.gz | tail
>> chr7A 736692151 . A T 30.4183 .
>> DP=2;VDB=0.32;SGB=-0.453602;MQ0F=0;AC=2;AN=2;DP4=0,0,0,2;MQ=32 GT:PL
>> 1/1:60,6,0
>> chr7A 736692161 . C T 30.4183 .
>> DP=2;VDB=0.32;SGB=-0.453602;MQ0F=0;AC=2;AN=2;DP4=0,0,0,2;MQ=32 GT:PL
>> 1/1:60,6,0
>> chr7A 736692407 . G C 16.3433 .
>> DP=5;VDB=0.22;SGB=-0.453602;RPB=1;MQB=1;BQB=1;MQ0F=0;ICB=1;
>> HOB=0.5;AC=1;AN=2;DP4=1,0,2,0;MQ=40
>> GT:PL 0/1:49,0,32
>> chr7A 736692408 . C T 59 .
>> DP=5;VDB=0.0983484;SGB=-0.511536;MQ0F=0;AC=2;AN=2;DP4=0,0,3,0;MQ=40
>> GT:PL 1/1:89,9,0
>> chr7A 736692435 . C G 106 .
>> DP=7;VDB=0.189048;SGB=-0.556411;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,3,1;MQ=37
>> GT:PL 1/1:136,12,0
>> chr7A 736692492 . G A 106 .
>> DP=7;VDB=0.184775;SGB=-0.556411;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,3,1;MQ=37
>> GT:PL 1/1:136,12,0
>> chr7A 736692503 . G A 15.355 .
>> DP=7;SGB=-0.379885;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;ICB=1;HOB
>> =0.5;AC=1;AN=2;DP4=2,1,1,0;MQ=37
>> GT:PL 0/1:48,0,75
>> chr7A 736692507 . T C 42.2273 .
>> DP=7;VDB=0.460446;SGB=-0.511536;RPB=1;MQB=1;MQSB=1;BQB=1;
>> MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=1,0,2,1;MQ=37
>> GT:PL 0/1:75,0,48
>> chr7A 736692530 . T C 15.2759 .
>> DP=6;SGB=-0.379885;RPB=1;MQB=1;MQSB=0;BQB=1;MQ0F=0;ICB=1;HOB
>> =0.5;AC=1;AN=2;DP4=1,2,1,0;MQ=39
>> GT:PL 0/1:48,0,82
>> chr7A 736692546 . A G 4.33255 .
>> DP=2;SGB=-0.379885;RPB=1;MQB=1;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC
>> =1;AN=2;DP4=0,1,0,1;MQ=44
>> GT:PL 0/1:35,0,23
>>
>>
>> Merged File
>> zgrep "chr7A" test.vcf | tail
>> chr7A 536773061 . T C 225 .
>> VDB=0.185719;SGB=-0.511536;MQ0F=0;MQ=60;MQSB=1;DP=13;DP4=0,
>> 0,2,9;AN=4;AC=4
>> GT:PL 1/1:102,9,0 1/1:255,24,0
>> chr7A 536773098 . T G 129 .
>> VDB=0.0243922;SGB=-0.616816;MQ0F=0;MQ=60;DP=7;DP4=0,0,0,6;AN=2;AC=2
>> GT:PL ./.:. 1/1:159,18,0
>> chr7A 536773112 . C T 112 .
>> VDB=0.0256605;SGB=-0.590765;MQ0F=0;MQ=60;DP=6;DP4=0,0,0,5;AN=2;AC=2
>> GT:PL ./.:. 1/1:142,15,0
>> chr7A 536773115 . G C 112 .
>> VDB=0.0256605;SGB=-0.590765;MQ0F=0;MQ=60;DP=5;DP4=0,0,0,5;AN=2;AC=2
>> GT:PL ./.:. 1/1:142,15,0
>> chr7A 536773513 . A G 225 .
>> VDB=0.0795616;SGB=-0.651104;MQSB=0;MQ0F=0;MQ=51;DP=23;DP4=0,
>> 0,15,4;AN=4;AC=4
>> GT:PL 1/1:211,24,0 1/1:255,33,0
>> chr7A 536773541 . C T 228 .
>> VDB=0.0660093;SGB=-0.662043;MQSB=0;MQ0F=0;MQ=52;RPB=1;MQB=1;
>> BQB=1;DP=30;DP4=0,1,18,4;AN=4;AC=4
>> GT:PL 1/1:244,27,0 1/1:255,1,0
>> chr7A 536773717 . A G 101 .
>> VDB=0.0860477;SGB=-0.511536;MQSB=1;MQ0F=0;MQ=52;DP=4;DP4=0,
>> 0,2,1;AN=2;AC=2
>> GT:PL 1/1:131,9,0 ./.:.
>> chr7A 536773733 . C G 101 .
>> VDB=0.0822145;SGB=-0.511536;MQSB=1;MQ0F=0;MQ=52;DP=4;DP4=0,
>> 0,2,1;AN=2;AC=2
>> GT:PL 1/1:131,9,0 ./.:.
>> chr7A 536773785 . A G 74 .
>> VDB=0.490096;SGB=-0.511536;MQSB=1;MQ0F=0;MQ=43;DP=3;DP4=0,0,1,2;AN=2;AC=2
>> GT:PL 1/1:104,9,0 ./.:.
>> chr7A 536773788 . T G 74 .
>> VDB=0.470313;SGB=-0.511536;MQSB=1;MQ0F=0;MQ=43;DP=3;DP4=0,0,1,2;AN=2;AC=2
>> GT:PL 1/1:104,9,0 ./.:.
>>
>>
>>
>> Is this a limitation of BCF tools, bgzip, or Tabix indexes? I've tried
>> using vcftools too, but obtained the same result. Are there any other
>> alternatives in order to merge this data together?
>>
>> Thank you for the help.
>>
>> Cheers,
>> -Hans
>>
>>
--
Hans Vasquez-Gross
<http://dubcovskylab.ucdavis.edu/lab-member/hans-vasquez-gross>
PhD Candidate
Dubcovsky Website - http://dubcovskylab.ucdavis.edu/
Department of Plant Science
University of California at Davis
Email: havasquezgr...@ucdavis.edu
Skype: hansvg.ucd
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