Hello Everyone,
I have been trying to transform a bcf file to vcf, using bcftools 0.1.19. - Basically, the following command works well with a test file (https://github.com/ecerami/samtools_primer/blob/master/tutorial/variants/sim_variants.bcf) as I get a small file with vcf characteristics:
bcftools view inputfile.bcf > outputfile.vcf
However, using the SAME command on hapmap SNP data (chr1-filtered-set-2014Apr15.bcf from http://www.medicagohapmap.org/downloads/mt40 ), gives me the following error:
Error in `bcftools': realloc(): invalid next size: 0x096d8d70
I googled a bit and it seems realloc() is related to memory, so I'm assuming my computer just doesnt have enough to deal with these data. However, I am not 100% sure this is the problem, so if anyone has tips or alternative ideas on this, I would be happy to read them. Thanks in advance!
At this point bcftoools v.0.1.19 is old. Try and use the latest (v.1.3) if you can. The command options have changed with new versions so take that into consideration if you do use the new version.
If it is indeed a memory issue then you may need to find a different computer to do this.