merge bams issue

[xuefenfei712]

Hey there

Thanks for Graphtyper, I am call SNPs but merged bams from the same individuals, and got the error below, can I know if you have any solutions,
TMPDIR=/disk/regine/data2/xuexue/tmp/ ~/software/graphtyper.27 genotype ref.fasta --sams=bam --region=chr15 --threads=10 --sams_index=bai

[2026-01-12 16:20:42.956] caller.cpp:2534 We found file with multiple samples, sorry, this is currently not supported.

but if I rename the header, I still got the issue below

base=$(basename "$bam" .bam)
out=fixed_bams/${base}.fixed.bam
echo "[FIXING] $bam -> SM=${base}"
samtools addreplacerg -r ID:${base} -r SM:${base} -r PL:ILLUMINA -r LB:${base} -r PU:${base} -o "$out" "$bam"
samtools index "$out"

[2026-01-12 16:34:29.330] hts_parallel_reader.cpp:309 Reads with name=f# both have IS_FIRST_IN_PAIR=1

Thankyou

Xue

[hannespetur]

I could suggest trying the --get_sample_names_from_filename option instead. This will make graphtyper ignore the "@rg" tag and just treat the filename ("base") as the sample name.