tabix query retruns multiple variants for a single position. Is it expected?

Question

[Ashis]

Hi,

I am trying to ask a query for a single position using tabix, but I am getting multiple variants in result. Interestingly, one variant's position is not same as my query position. I wonder if its expected, or if there is any way to avoid such scenario.

My query is like below:

tabix chr.all.vcf.bgz 9:136131322-136131322

Result looks like below:

9    136127800    MERGED_DEL_2_55992    TCCCCCAGGGAGGCGGGGCGCAGGGATTGCAGTGAGGCCCTGTGCCCAGGCTGGCTGTGCCCTACCTGCGGGAAGAGTCACTCCAGTCCCTCTGGGCTGGTCCAGGTGCAACCACAGTAGGACACAGGTCAACTCCAGTGAAATGTGGAGGGAGGAAGGGTGTGCCTGCCTGCTCCTTCCCCTCCCTTGCAGGGAGGGGCGGTTGCCCTCAGCAACAGAATGCCCACGTGGGATACTGGAAGCTTCAGCTTACCCCACCCCACCCCTCCAGGCCCGGTTTGTCCTGGGCGCAAGGGGCTACTTCAGAGCTGCCAGGCCTCCACAGCAACACATTAAATGTTCTGGAAACTAGGAGATGTGGCACTGCTGTACAACGGTCAGGAATAGCCATCCTGTCCTCCTGACCCGGTGAAAACCAGCTTCTGCTGGGAAGGAGCATGGGGTGGCGCCTGGCTTTTGGAGTCAGGAAGAACCAGGCTTAAGTAATAGAACTGCCTGACCTCCAGCTTGTCTCTTCAGCTCCCAGGTCTGTGCTCGATTTGGGATTATTGGGTGGGGCACATAAGAAGCTGCGTTCTGTGCTCTCAGGGTGCTGGACGCTGTTTCAGGTACCAGTACACACCAGAGGGAAGAGAGTGCCTGATGGCATGGTGATTGATTTTAGTGGAGACAGCTAGACACTAAACCAGGAGTTCTGTCATGCCAGTTGGTGATAAATTGATTTCTTGAAGATTTTTCCACTTCCAAGCAAGGTAGAATAGATGCACCTGTCCCCACGCCCTACACTAAGGACAGTTAAAATCTCTGTATATTTCCCTGGGTATTACACATACATATATAACTACATACATAAACGTATGTATATCAAACACTAAAAGGTGGAGAGAAGAAGGCAGACCATGTAGGGACCTTGGGACCTGAGGAATGACATGACAGGAGTTCCCTGGGTTTTCTTTCTGCCTCATATATCTGTGACTGTGTGCTGGAAAAGCCAGCAACACGAAACACCAAAAGACACAGACAAAAACCAACAACAACAAACCCAACAAGTTGGCCCTCAGCCAAAATAATTAGGCAAGAGGAAGAAATAAAAGGTATCCAAATTGGAAAGGAAGAACTTAAATTGTCCCTGTTTACAGATGACATGATCTTATAGAAAACCCTAAAGATTCCACCAATAAGATGTTAGAATAAATGAAATCAGTAAAGTTGCAGGATATAAAATTAACATACAACAATCTGTAGCATTTCTATACCCTAACAAAGAAATCAAGAAAACAATGTCATTTACAATAGCTACAAAAAATACTTGCAAATAAATCCAACCAAGGAAGTGAAAGATCTGTATGCTGAAAACTATAAAACATTTGTGAAAGAAATTGAAGATACAAATAATTAGAAAGCTGTCCCATATCTGAGATCAGGTGCCAAAAAAAAGACATCCCATGTTCATGAATTGGAAGAATTAATATTGTTAAAATGTCCATACAACCCCAAACAATCTACAGATTCAATGCAATCCCTATCAAAATTTCATTGACATTTTTCACTGAAATAAATAAAATAATCCTAAAATTCGTATGAGGGAGTAACACCTGCTCCACAGTGGCACAAAGCACTGTCAGGTGCCACACACAGCCTGTTGGGACATGTGGGCCACAGTACTTCCCCACCTAAAGTACTGTAGAGGCCCAGGAGACATGAGCCAGGGCCATTTTAACTGTCAGTAATGGCCACAAAGACCCCTAAATAGCCAAAGCAATCTTAAGCAAAAAGAACAAAGCTGGAGACAATACACTACCTAACTTCAAGATATACTATAAAGCTATAATAATCAAAACATCATGGTATTGGCATAAAAACAAACAGACCAATGAAACAGAATAGAGAGCCCGGAAGTGAATCCATGCATTTACGGTCAACTGATTTTTGACAGAAATGCCAAGAAACACAATGTGGAAACGACAGTCTGTTCAATAAATGATGTTGGGGCCAGGTGCAGTGGCTCATGCTTATAATCCTAGCACTTTGGGATGCCGAGGTGGAAGGACCACTTGAGGCCTCCCTCCAGGCTCCGGAAGAGACCTCCTCCATGATCCCTTGTCTAAGGGGAAGGTTCCTCAGGACCTTACCGTGGGGGCTGAAGGTGGCCACCCCTCCAGGAACTTATGCCCCAGGCGCTGAATTTGGGCTGCCTAAGTCTGTGTGCGTGAGTCTGTGTTTGTGTGCATGTCTGCATGTCTGTGTGTTTGCATGCATGTCTGTGTGTCTGTGTGGTCTATGTGTCTGTGTGTACACTTCTGTATGTCTTTCTCTGTGCATTTTTGCATGTGTCTCCATGTGTCTCTGTGCATGTCTGTGTGTCTATATGTCTGTGTCTTTGTATCTGTGTATCTGTGTCTGTGTGTCTTTGCGTGTCTGGTGTATGTCTGTGTGTGTGTGTATGTCTGTGTATGTAACGGTGTGTCTCTGTGGCGGGGGGTGTGTGTGTGATTGTGTGTGTGTGTGTGTCTGTGTATGTAATGGTGTGTCTCTGTGGCGGGGAGGGGCTGTGTGTGTCTTTCTGTGTATGTGTGTGTAACGGTGTGTCTCTATGGCCGGGAGGGGGTATCTGTGATTGTGTGTCTGTGTGTGTCTGTGTATGTAATGGTGTGTCTCTGTGGCGGGGAGGGGCTGTGTGTGATTGTGTGTCTGTGTGTGTCTGTGTATGTAATGGTGTGTCTCTGTGGCGGGGAGGGTGTGTGTGTGATTTTGTGTCTGTGTGTGTCTTTCTGTGTGTGTCTGTGTATGTAATGGTGTGTCTCTGTGGCGGGGAGGGGCTGCGTGTGATTGTGTGTCTGTGTGTGTCTTTCTGTGTATGTGTGTGTAATGGTGTGTTTCTGTGGCCGGAAGGGCGTATCTGCGATTGCGTGTCTGTGTATGTAATGGTGTGTCTCTGTGGCGGGGAGGGTGTGTGTGTGATTTTGTGTCTGTGTCTTTCTGTGTGTGTCTGTGTATGTAATGGTGTCTCTGTGGCGGGGAGGGTGTGTGTGTGATTTTGTGTCTGTGTGTGTCTTTCTGTGTGTGTCTGTGTATGTAATGGTGTCTCTGTGGTGGGGAGGGGGTGTGTGTGATTTGAGGTGGGGACGGGGCCTAGGCTTCAGTTACTCACAACAGGACGGACAAAGGAAACAGAGTTTACCCGTTCTGCTAAAACCAAGGGCGGGAGGGGGACGGGGCTGCCGGCAGCCCTCCCAGAGCCCCTGGCAGCCGCTCACGGGTTCCGGACCGCCTGGTGGTTCTTGGGCACCGCAGTGAACCTCAGCTTCCTCAGGACGGCGGGCCAGCCCAGCAGCTGCTGGTCCCACAAGTACTCGGGGGAGAGCACCTTGGTGGGTTTGTGGCGCAGCAGGTACTTGTTCAGGTGGCTCTCGTCGTGCCACACGGCCTCGATGCCGTTGGCCTGGTCGACCATCATGGCCTGGTGGCAGGCCCTGGTGAGCCGCTGCACCTCTTGCACCGACCCCCCGAAGAACCCCCCCAGGTAGTAGAAATCGCCCTCGTCCTTGGGGATGTAGGCCTGGGACTGGGGCCGGCGCTCGTAGGTGAAGGCCTCCCGGCTGCTTCCGTAGAAGCCGGGGTGCAGGGTGCCGAACAGCGGAGTCAGGATCTCCACGCCCACGTGGTCGCGGAACTCCATGTCCACGTCCACGCACACCAGGTAATCCACCTCGCTGAGGAAGCGCCGCTCGCAGAAGTCACTGATCATCTCCATGCGGCGCATGGACACGTCCTGCCAGCGCTTGTAGGCGCGCACCTCCAGCACTGACAGCTGCCGACCGGTCCCCAGCGTCACGCGGGGCACCGCGGCCGGCTGGTCGGTGAAGACATAGTAGTGGACACGGTGGCCCACCATGAAGTGCTTCTCCGCCGTCTCCAGGAACAGCTTCAGGAAAGCCACGTATCTGCAAGGCAGGCGGACGGGGGCTGGGGGAGCCGCCGGCCGTGCACCCCTGGGCTGCAGGAGGCCCGTCCTGCACCCGCCCGCCAGCGGCCATTGGAAGGCTTAGAGCAGCAGATGCACCACGTTCTCCTGCCCTGTCCTGAGCGAGTCCTCGGGCTGCGATTCACTTCATCCTCTTCCCAGCGATGGGGGACCACCAGCACCCCCTCTTACTAAGGAGGGCTGAGGGCAGGTGGCTGGAGGCTGGTAGCAGGCCGCAGGCTGGCGTCTGCTCACTCCCCCTCAGCCTGGCCTGAGCCACGCCTCCCCACGCAGCTGCCCCTCTTATGGCCAGGCCGGCCACGTGCTCCCTCATTATAAGCTGCACGCGAGGCCTCCACACACCCGCCTCTGCACCCTAGAGCTTCCTCCCTCCAGGCTTGAACTGCACCTATTCCTAAGAGTAAGTCATTCCTGGCCTCCGCCACTGTCGCTGGCCCAGCTGCCCACAGCTGCCGAGAAGTCAAGTATGTGTCTGCGGTTGCCTGGCTAGCTCCCTCTCTGGCCTGGCCCAGAGTCCCAGGGCCTTGTGGGTCAGCCACTTCCTTTGGTGTCTGGGGCCAACTGCTTTGCCTGCCCCACCTACATCTGACAGAGAAGTGACCACGGCTCTGCCAGCATCCTCTTTCTAGGGTCCAAGGACAGCAAACAGGTGTCCCCCTCCTGCTATCTCTGGTCAGTGAGCAGGAAACATCTGGAGCCTTGTATTGAGGGGGTGGCTCAGCATGACGGCCGGCCACAGTTACAGAGAGGAGGGGGCAGCAGAAGCCACCATCCCTGGGTGAGACGCAGCCTCTGGAGAAGGAGCTGGGTTTTACCGACCTGGCGAGCCCACGAGCCCACGAGCCCACATGAGCTCAGTAAGATGCTGCATGAATGACCTTTCCCATCTACCCTCTGGGAGGACAAGGCTGGCCGCCACCCCACTCTGTCTTGAACACAAGGAGAGACCTCAATGTCCACAGTCACTCGCCACTGCCTGGGTCTCTACCCTCGGCCACCTCACTGACTTACTTCTTGATGGCAAACACAGTTAACCCAATGGTGGTGTTCTGGAGCCTGAACTGCTCGTTGAGGATGTCGATGTTGAATGTGCCCTCCCAGACAATGGGAGCCAGCCAAGGGGTACCACGAGGACATCCTTCCTACTGCACATGGAGAGAGGCGTGCGGTCACATGGAGCTGGCAGGGTGCCACCCACATGCGCCTCTGGCACACGGCCGCCCCCACCTGGAAACTCCACTCAGCTTCTGCCTCCTCTGACCACCCTTCCAGAGGCAGCCGCCCTTCCCCGGGAAACCAACCAGAGGCAAATGCGACTCCAACCGGGCAAATCATTCCCAGCCCTCCCTCAACATTGGACCTGTGGGAACACACAGCAAGCTGAGCTTTGCTGGCAAAGAGATAGGAACAAACCCTCCCCAGCACCCAACCCCCGCTGCCCCTCCCCAGGTAGGAGGTACCTATCAGGCCTTTGCAGGGGCTTTGGAGAACAAAGGGACAGGAAACAAGAGACGCAAGTCAGAGAAAGCAAAGGGAAAGAGGACAGCCATGTGGGCCTCTGAATTCAGATGTCAGGAGAATCTGAGAGGAGAGAACGGGGAAGCAGCCCCAACTGAGATTTACATCAAGGAAACCGCCCTCTAATACCTTCAGAACAGCCCCTTGAGCTGCGTTCAGTTTCAGTGTCAGTAACTTTACTCACCACGGTGTCAGCACCTTTGACTGGGGGTAGACCATCCTGCAAGCACAAAGCGCCGCCACGTGAGTTTGCATGGAAAGCGTGGGATGCAGGTAAGCAGGGGGTGTGCACAGCCGCTGAACCATGACTGGGCATTGA    T    .    info4;maf05    EXP_FREQ_A1=0.000;IMPINFO=0.000;CERTAINTY=1.000;TYPE=0;MISS=0;HW=1    GL:GT:DS    1,0,0:0/0:0    1,0,0:0/0:0    1,0,0:0/0:0    1,0,0:0/0:0    1,0,0:0/0:0    1,0,0:0/0:0    1,0,0:0/0:0    1,0,0:0/0:0    1,0,0:0/0:0    1,0,0:0/0:0    1,0,0:0/0:0    1,0,0:0/0:0    1,0,0:0/0:0    1,0,0:0/0:0    1,0,0:0/0:0    

9    136131322    rs8176746    G    T    .    PASS    EXP_FREQ_A1=0.100;IMPINFO=1.000;CERTAINTY=1.000;TYPE=2;MISS=0;HW=0.60587    GL:GT:DS    1,0,0:0/0:0    1,0,0:0/0:0    1,0,0:0/0:0    0,1,0:0/1:1    1,0,0:0/0:0    1,0,0:0/0:0    0,1,0:0/1:1    1,0,0:0/0:0    1,0,0:0/0:0    0,1,0:0/1:1    1,0,0:0/0:0    1,0,0:0/0:0    1,0,0:0/0:0    1,0,0:0/0:0    0,1,0:0/1:1 

[Ashis]

I just realized that the ref and alt alleles' lengths are 5822 and 1, respectively in the first variant. And first variant's position (136127800) is within 5822 bp from my query position (136131322). Is it the reason I am getting multiple variants for my query position?

I am actually interested about SNPs. I would appreciate if anyone can suggest a way get only snps from tabix, without post-processing tabix result (I can do this).

Answer 1

[Ying W]

So the first variant (the super long one) is a deletion that spans the region you are interested in.

The second variant is a SNP (G->T) at the location you are interested in

You can use bcftools (successor to vcftools, click on the manual link on the left) and look at the options under filter to remove all non-snps

Answer 2

[slw287r]

try re-index your vcf.bgz with tabix with -b and -e specified, not sure if it helps