xiaoshanpai
commented
2 months ago The 10X website says that data with Visium for fresh-frozen can called SNPS（https://kb.10xgenomics.com/hc/en-us/articles/6325542905229-Visium-CNV-calling）, and the description of the data says that the data has transcripts
hello，When I used data with Visium for fresh-frozen from https://www.10xgenomics.com/cn/datasets/fresh-frozen-visium-on-cytassist-human-breast-cancer-probe-based-whole-transcriptome-profiling-2-standard , it still couldn't call SNPS
Here are some related logs：
[I::main] end time: 2024-03-18 17:47:19 [I::main] time spent: 510 seconds. character(0) Creating VCFs No SNPs left for chr2! No SNPs left for chr4! No SNPs left for chr7! No SNPs left for chr10! No SNPs left for chr11! No SNPs left for chr13! No SNPs left for chr14! No SNPs left for chr17! No SNPs left for chr18! No SNPs left for chr20! [1] 0 Running phasing --> WARNING: Check REF/ALT agreement between target and ref? <-- ERROR: Unable to open file: ./numbat/phasing/breast_chr2.vcf.gz --> WARNING: Check REF/ALT agreement between target and ref? <--
ERROR: Target and ref have too few matching SNPs (M = 0) ERROR: Unable to open file: ./numbat/phasing/breast_chr4.vcf.gz --> WARNING: Check REF/ALT agreement between target and ref? <--
ERROR: Target and ref have too few matching SNPs (M = 0) --> WARNING: Check REF/ALT agreement between target and ref? <--
ERROR: Target and ref have too few matching SNPs (M = 0) ERROR: Unable to open file: ./numbat/phasing/breast_chr7.vcf.gz --> WARNING: Check REF/ALT agreement between target and ref? <--
ERROR: Target and ref have too few matching SNPs (M = 0) --> WARNING: Check REF/ALT agreement between target and ref? <--
ERROR: Target and ref have too few matching SNPs (M = 0) ERROR: Unable to open file: ./numbat/phasing/breast_chr10.vcf.gz ERROR: Unable to open file: ./numbat/phasing/breast_chr11.vcf.gz --> WARNING: Check REF/ALT agreement between target and ref? <--
ERROR: Target and ref have too few matching SNPs (M = 0) ERROR: Unable to open file: ./numbat/phasing/breast_chr13.vcf.gz ERROR: Unable to open file: ./numbat/phasing/breast_chr14.vcf.gz --> WARNING: Check REF/ALT agreement between target and ref? <--
ERROR: Target and ref have too few matching SNPs (M = 0) --> WARNING: Check REF/ALT agreement between target and ref? <--
ERROR: Target and ref have too few matching SNPs (M = 0) ERROR: Unable to open file: ./numbat/phasing/breast_chr17.vcf.gz ERROR: Unable to open file: ./numbat/phasing/breast_chr18.vcf.gz --> WARNING: Check REF/ALT agreement between target and ref? <--
ERROR: Target and ref have too few matching SNPs (M = 0) ERROR: Unable to open file: ./numbat/phasing/breast_chr20.vcf.gz --> WARNING: Check REF/ALT agreement between target and ref? <--
ERROR: Target and ref have too few matching SNPs (M = 0) --> WARNING: Check REF/ALT agreement between target and ref? <--
ERROR: Target and ref have too few matching SNPs (M = 1) Generating allele count dataframes Error in FUN(X[[i]], ...) : Phased VCF not found Calls: %>% -> mutate -> Reduce -> lapply -> FUN Execution halted