Bcftools concat gives chromosome contiguous error?

Question

[vctrm67]

I am trying to merge vcfs from GATK's Mutect with bcftools, however I keep getting this message:

The chromosome block 9 is not contiguous, consider running with -a.

I have tried sorting with vcf-tools but I keep getting the same error. Does anyone have any suggestions?

[finswimmer]

Hello vctrm67 ,

can you please show us the command you have used? Furthermore use bcftools sort instead of vcftools, because vcftools is deprecated.

fin swimmer

[vctrm67]

I used:

for file in *.intervals.vcf; do bcftools sort $file -o ${file}.test.vcf ; done

Then I used:

bcftools concat *.test.vcf -o test.vcf

[WouterDeCoster]

And did that help?

[Kevin Blighe]

How are your contigs ('chromosomes') named? - check the VCF header via bcftools view -h

[vctrm67]

According to the human_g1k_v37 reference. This is the header:

##contig=<ID=1,length=249250621,assembly=b37>
##contig=<ID=2,length=243199373,assembly=b37>
##contig=<ID=3,length=198022430,assembly=b37>
##contig=<ID=4,length=191154276,assembly=b37>
##contig=<ID=5,length=180915260,assembly=b37>
##contig=<ID=6,length=171115067,assembly=b37>
##contig=<ID=7,length=159138663,assembly=b37>
##contig=<ID=8,length=146364022,assembly=b37>
##contig=<ID=9,length=141213431,assembly=b37>
##contig=<ID=10,length=135534747,assembly=b37>
##contig=<ID=11,length=135006516,assembly=b37>
##contig=<ID=12,length=133851895,assembly=b37>
##contig=<ID=13,length=115169878,assembly=b37>
##contig=<ID=14,length=107349540,assembly=b37>
##contig=<ID=15,length=102531392,assembly=b37>
##contig=<ID=16,length=90354753,assembly=b37>
##contig=<ID=17,length=81195210,assembly=b37>
##contig=<ID=18,length=78077248,assembly=b37>
##contig=<ID=19,length=59128983,assembly=b37>
##contig=<ID=20,length=63025520,assembly=b37>
##contig=<ID=21,length=48129895,assembly=b37>
##contig=<ID=22,length=51304566,assembly=b37>
##contig=<ID=X,length=155270560,assembly=b37>
##contig=<ID=Y,length=59373566,assembly=b37>
##contig=<ID=MT,length=16569,assembly=b37>
##contig=<ID=GL000207.1,length=4262,assembly=b37>
##contig=<ID=GL000226.1,length=15008,assembly=b37>
##contig=<ID=GL000229.1,length=19913,assembly=b37>
##contig=<ID=GL000231.1,length=27386,assembly=b37>
##contig=<ID=GL000210.1,length=27682,assembly=b37>
##contig=<ID=GL000239.1,length=33824,assembly=b37>
##contig=<ID=GL000235.1,length=34474,assembly=b37>
##contig=<ID=GL000201.1,length=36148,assembly=b37>
##contig=<ID=GL000247.1,length=36422,assembly=b37>
##contig=<ID=GL000245.1,length=36651,assembly=b37>
##contig=<ID=GL000197.1,length=37175,assembly=b37>
##contig=<ID=GL000203.1,length=37498,assembly=b37>
##contig=<ID=GL000246.1,length=38154,assembly=b37>
##contig=<ID=GL000249.1,length=38502,assembly=b37>
##contig=<ID=GL000196.1,length=38914,assembly=b37>
##contig=<ID=GL000248.1,length=39786,assembly=b37>
##contig=<ID=GL000244.1,length=39929,assembly=b37>
##contig=<ID=GL000238.1,length=39939,assembly=b37>
##contig=<ID=GL000202.1,length=40103,assembly=b37>
##contig=<ID=GL000234.1,length=40531,assembly=b37>
##contig=<ID=GL000232.1,length=40652,assembly=b37>
##contig=<ID=GL000206.1,length=41001,assembly=b37>
##contig=<ID=GL000240.1,length=41933,assembly=b37>
##contig=<ID=GL000236.1,length=41934,assembly=b37>
##contig=<ID=GL000241.1,length=42152,assembly=b37>
##contig=<ID=GL000243.1,length=43341,assembly=b37>
##contig=<ID=GL000242.1,length=43523,assembly=b37>
##contig=<ID=GL000230.1,length=43691,assembly=b37>
##contig=<ID=GL000237.1,length=45867,assembly=b37>
##contig=<ID=GL000233.1,length=45941,assembly=b37>
##contig=<ID=GL000204.1,length=81310,assembly=b37>
##contig=<ID=GL000198.1,length=90085,assembly=b37>
##contig=<ID=GL000208.1,length=92689,assembly=b37>
##contig=<ID=GL000191.1,length=106433,assembly=b37>
##contig=<ID=GL000227.1,length=128374,assembly=b37>
##contig=<ID=GL000228.1,length=129120,assembly=b37>
##contig=<ID=GL000214.1,length=137718,assembly=b37>
##contig=<ID=GL000221.1,length=155397,assembly=b37>
##contig=<ID=GL000209.1,length=159169,assembly=b37>
##contig=<ID=GL000218.1,length=161147,assembly=b37>
##contig=<ID=GL000220.1,length=161802,assembly=b37>
##contig=<ID=GL000213.1,length=164239,assembly=b37>
##contig=<ID=GL000211.1,length=166566,assembly=b37>
##contig=<ID=GL000199.1,length=169874,assembly=b37>
##contig=<ID=GL000217.1,length=172149,assembly=b37>
##contig=<ID=GL000216.1,length=172294,assembly=b37>
##contig=<ID=GL000215.1,length=172545,assembly=b37>
##contig=<ID=GL000205.1,length=174588,assembly=b37>
##contig=<ID=GL000219.1,length=179198,assembly=b37>
##contig=<ID=GL000224.1,length=179693,assembly=b37>
##contig=<ID=GL000223.1,length=180455,assembly=b37>
##contig=<ID=GL000195.1,length=182896,assembly=b37>
##contig=<ID=GL000212.1,length=186858,assembly=b37>
##contig=<ID=GL000222.1,length=186861,assembly=b37>
##contig=<ID=GL000200.1,length=187035,assembly=b37>
##contig=<ID=GL000193.1,length=189789,assembly=b37>
##contig=<ID=GL000194.1,length=191469,assembly=b37>
##contig=<ID=GL000225.1,length=211173,assembly=b37>
##contig=<ID=GL000192.1,length=547496,assembly=b37>