Hello, I am trying to merge two vcf files with bcftools. These are the commands I am using:
/bcftools merge -m id -o merged.vcf.gz pop1.vcf.gz pop2.vcf.gz

I get the following message:

The REF prefixes differ: T vs C (1,1)
Failed to merge alleles at 10:252693 in /path/merged.vcf.gz

Any help would be very welcome ! Thanks very much in advance

These are the headers of the 2 files and some samples:

pop1.vcf.gz:

##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##filedate=20180903
##source="beagle.jar (r1399)"
##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated Allele Frequencies">
##INFO=<ID=AR2,Number=1,Type=Float,Description="Allelic R-Squared: estimated correlation between most probable ALT dose and true ALT dose">
##INFO=<ID=DR2,Number=1,Type=Float,Description="Dosage R-Squared: estimated correlation between estimated ALT dose [P(RA) + 2*P(AA)] and true ALT dose">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##contig=<ID=10>
##bcftools_annotateVersion=1.9+htslib-1.9
##bcftools_annotateCommand=annotate -x FORMAT/DS,FORMAT/GP -o /path/pop1_195_10_GT.vcf /path/pop1_195_10_phased.vcf.gz; Date=Tue Sep 4 15:50:41 2018
##contig=<ID=11>
##contig=<ID=12>
##contig=<ID=13>
##contig=<ID=14>
##contig=<ID=15>
##contig=<ID=16>
##contig=<ID=17>
##contig=<ID=18>
##contig=<ID=19>
##contig=<ID=1>
##contig=<ID=20>
##contig=<ID=21>
##contig=<ID=22>
##contig=<ID=2>
##contig=<ID=3>
##contig=<ID=4>
##contig=<ID=5>
##contig=<ID=6>
##contig=<ID=7>
##contig=<ID=8>
##contig=<ID=9>
##bcftools_concatVersion=1.9+htslib-1.9
##bcftools_concatCommand=concat path/pop1_195_10_GT.vcf.gz /path/pop1_195_11_GT.vcf.gz /path/pop1_195_12_GT.vcf.gz /path/pop1_195_13_GT.vcf.gz /path/pop1_195_14_GT.vcf.gz /path/pop1_195_15_GT.vcf.gz /path/pop1_195_16_GT.vcf.gz /path/pop1_195_17_GT.vcf.gz /path/pop1_195_18_GT.vcf.gz /path/pop1_195_19_GT.vcf.gz /path/pop1_195_1_GT.vcf.gz /path/pop1_195_20_GT.vcf.gz /path/pop1_195_21_GT.vcf.gz /path/pop1_195_22_GT.vcf.gz /path/pop1_195_2_GT.vcf.gz /path/pop1_195_3_GT.vcf.gz //path/pop1_195_4_GT.vcf.gz /path/pop1_195_5_GT.vcf.gz /path/pop1_195_6_GT.vcf.gz /path/pop1_195_7_GT.vcf.gz /path/pop1_195_8_GT.vcf.gz /path/pop1_195_9_GT.vcf.gz; Date=Tue Sep 4 16:13:54 2018
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT spa_1 spa_2 spa_3
10 144847 rs11253478 C T . PASS AR2=1;DR2=1;AF=0.082 GT 0|0 0|0 0|1
10 244561 rs2448366 G A . PASS AR2=1;DR2=1;AF=0.446 GT 1|1 0|1 0|0
10 252693 rs2379078 T C . PASS AR2=1;DR2=1;AF=0.238 GT 0|0 0|0 0|1

Pop2:

##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##filedate=20180830
##source="beagle.jar (r1399)"
##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated Allele Frequencies">
##INFO=<ID=AR2,Number=1,Type=Float,Description="Allelic R-Squared: estimated correlation between most probable ALT dose and true ALT dose">
##INFO=<ID=DR2,Number=1,Type=Float,Description="Dosage R-Squared: estimated correlation between estimated ALT dose [P(RA) + 2*P(AA)] and true ALT dose">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##contig=<ID=10>
##bcftools_annotateVersion=1.9+htslib-1.9
##bcftools_annotateCommand=annotate -x FORMAT/DS,FORMAT/GP -o /path/pop2_10_GT.vcf /path/pop2_10_phased.vcf.gz ' '; Date=Tue Sep 4 12:38:31 2018
##contig=<ID=11>
##contig=<ID=12>
##contig=<ID=13>
##contig=<ID=14>
##contig=<ID=15>
##contig=<ID=16>
##contig=<ID=17>
##contig=<ID=18>
##contig=<ID=19>
##contig=<ID=1>
##contig=<ID=20>
##contig=<ID=21>
##contig=<ID=22>
##contig=<ID=2>
##contig=<ID=3>
##contig=<ID=4>
##contig=<ID=5>
##contig=<ID=6>
##contig=<ID=7>
##contig=<ID=8>
##contig=<ID=9>
##bcftools_concatVersion=1.9+htslib-1.9
##bcftools_concatCommand=concat /path/pop2_10_GT.vcf.gz /path/pop2_11_GT.vcf.gz /path/pop2_12_GT.vcf.gz /path/pop2_13_GT.vcf.gz /path/pop2_14_GT.vcf.gz /path/pop2_15_GT.vcf.gz /path/pop2_16_GT.vcf.gz /path/pop2_17_GT.vcf.gz /path/pop2_18_GT.vcf.gz /path/pop2_19_GT.vcf.gz /path/pop2_1_GT.vcf.gz /path/pop2_20_GT.vcf.gz /path/pop2_21_GT.vcf.gz /path/pop2_22_GT.vcf.gz /path/pop2_2_GT.vcf.gz /path/pop2_3_GT.vcf.gz /path/pop2_4_GT.vcf.gz /path/pop2_5_GT.vcf.gz /path/pop2_6_GT.vcf.gz /path/pop2_7_GT.vcf.gz /path/pop2_8_GT.vcf.gz /path/pop2_9_GT.vcf.gz; Date=Tue Sep 4 16:14:14 2018
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ind_1 ind_2 ind_3
10 144847 rs11253478 C T . PASS AR2=1;DR2=1;AF=0.474 GT 0|0 0|1 0|0
10 244561 rs2448366 G A . PASS AR2=1;DR2=1;AF=0.321 GT 1|1 1|0 0|1
10 252693 rs2379078 C T . PASS AR2=1;DR2=1;AF=0.359 GT 1|1 1|0 0|1