seqMerge error - File 2: chromosomes and positions are unsorted.

[boboppie]

Dear @zhengxwen / @zhengxw-ab ,

Hope you are keeping well.

I was trying to merge two samples:
seqMerge(c("sample_1.gds", "sample_2.gds"), "merged.gds", storage.option="LZMA_RA", verbose=TRUE))

error:

Error in seqMerge(c(""sample_1.gds", "sample_2.gds"), :
File 2: chromosomes and positions are unsorted.`

Some additional info:

f1 <- seqOpen("sample_1.gds")
f2 <- seqOpen("sample_2.gds")
head(seqGetData(f, "$chrom_pos"))
[1] "1:10230" "1:10247" "1:10329" "1:10352" "1:10469" "1:10519"
head(seqGetData(f2, "$chrom_pos"))
[1] "1:10230" "1:10329" "1:10352" "1:10745" "1:10774" "1:14455"

This looks similar to #41, but I've made sure to sort the VCFs first using bcftools sort. Those two samples do not share the exact same variants, should seqMerge work in this case?

Many thanks in advance.

Best wishes,
Fengyuan

[zhengxwen]

seqMerge() needs the same samples or the same variants to merge the files.

Why not use bcftools to merge the VCF files?

[zhengxwen]

SeqArray_1.44.1 (702488b) should fix this question.