Genotyping ATAC from WES vcf

[ollieeknight]

Heya,

I'm trying to genotype around 3.5k cells from a 10x multiome run using the ATAC portion of the experiment, with a paired filtered WES vcf file containing around 100 variants.

cellsnp-lite -s multi/data/s1/outs/atac_possorted_bam.bam -b multi/data/s1/outs/filtered_feature_bc_matrix/barcodes.tsv.gz -O genotype -R wes_outs/mutect2/annotation/mutect2/s452_vs_si452/output.vcf -p 32 --minMAF 0 --minCOUNT 1 --UMItag None --gzip

It completes in less than 0s, and the size of the genotype folder is 512kb, and when I load the AD matrix into R it's just a field of zeros. Do you have any advice to help me get this going?

Thanks a million

Ollie

[hxj5]

Hi Ollie,

Are there any SNPs outputed, i.e., cellSNP.base.vcf.gz contains any SNPs or the DP matrix has any non-zero values? Can you share more detailed logging information (just want to check if cellsnp-lite worked well)?

Xianjie

[ollieeknight]

yep, apologies! genotype.zip

[hxj5]

thanks for sharing the folder. There are 64 SNPs outputed (in the VCF file), while the number of SNPs in every matrix is zero. There should be some errors. You may change the output directory and re-run the cmdline. It would be helpful if you could save the logging information and share it here.

[ollieeknight]

from running the same command I initally posted,

Out log

``` [I::main] start time: 2023-02-27 11:56:26 [W::check_args] Max depth set to maximum value (2147483647) [I::main] loading the VCF file for given SNPs ... [I::main] fetching 98 candidate variants ... [I::main] mode 1a: fetch given SNPs in 3867 single cells. [W::hts_idx_load3] The index file is older than the data file: multi/data/s1/outs/atac_possorted_bam.bam.bai [I::csp_fetch_core][Thread-2] 33.33% SNPs processed. [I::csp_fetch_core][Thread-4] 33.33% SNPs processed. [I::csp_fetch_core][Thread-4] 66.67% SNPs processed. [I::csp_fetch_core][Thread-20] 33.33% SNPs processed. [I::csp_fetch_core][Thread-14] 33.33% SNPs processed. [I::csp_fetch_core][Thread-10] 33.33% SNPs processed. [I::csp_fetch_core][Thread-31] 33.33% SNPs processed. [I::csp_fetch_core][Thread-26] 33.33% SNPs processed. [I::csp_fetch_core][Thread-14] 66.67% SNPs processed. [I::csp_fetch_core][Thread-7] 33.33% SNPs processed. [I::csp_fetch_core][Thread-11] 33.33% SNPs processed. [I::csp_fetch_core][Thread-7] 66.67% SNPs processed. [I::csp_fetch_core][Thread-2] 66.67% SNPs processed. [I::csp_fetch_core][Thread-16] 33.33% SNPs processed. [I::csp_fetch_core][Thread-28] 33.33% SNPs processed. [I::csp_fetch_core][Thread-28] 66.67% SNPs processed. [I::csp_fetch_core][Thread-24] 33.33% SNPs processed. [I::csp_fetch_core][Thread-16] 66.67% SNPs processed. [I::csp_fetch_core][Thread-27] 33.33% SNPs processed. [I::csp_fetch_core][Thread-27] 66.67% SNPs processed. [I::csp_fetch_core][Thread-9] 33.33% SNPs processed. [I::csp_fetch_core][Thread-3] 33.33% SNPs processed. [I::csp_fetch_core][Thread-20] 66.67% SNPs processed. [I::csp_fetch_core][Thread-18] 33.33% SNPs processed. [I::csp_fetch_core][Thread-31] 66.67% SNPs processed. [I::csp_fetch_core][Thread-25] 33.33% SNPs processed. [I::csp_fetch_core][Thread-25] 66.67% SNPs processed. [I::csp_fetch_core][Thread-24] 66.67% SNPs processed. [I::csp_fetch_core][Thread-8] 33.33% SNPs processed. [I::csp_fetch_core][Thread-5] 33.33% SNPs processed. [I::csp_fetch_core][Thread-10] 66.67% SNPs processed. [I::csp_fetch_core][Thread-19] 33.33% SNPs processed. [I::csp_fetch_core][Thread-9] 66.67% SNPs processed. [I::csp_fetch_core][Thread-17] 33.33% SNPs processed. [I::csp_fetch_core][Thread-30] 33.33% SNPs processed. [I::csp_fetch_core][Thread-30] 66.67% SNPs processed. [I::csp_fetch_core][Thread-19] 66.67% SNPs processed. [I::csp_fetch_core][Thread-22] 33.33% SNPs processed. [I::csp_fetch_core][Thread-12] 33.33% SNPs processed. [I::csp_fetch_core][Thread-23] 33.33% SNPs processed. [I::csp_fetch_core][Thread-18] 66.67% SNPs processed. [I::csp_fetch_core][Thread-11] 66.67% SNPs processed. [I::csp_fetch_core][Thread-22] 66.67% SNPs processed. [I::csp_fetch_core][Thread-8] 66.67% SNPs processed. [I::csp_fetch_core][Thread-1] 25.00% SNPs processed. [I::csp_fetch_core][Thread-1] 50.00% SNPs processed. [I::csp_fetch_core][Thread-3] 66.67% SNPs processed. [I::csp_fetch_core][Thread-21] 33.33% SNPs processed. [I::csp_fetch_core][Thread-5] 66.67% SNPs processed. [I::csp_fetch_core][Thread-12] 66.67% SNPs processed. [I::csp_fetch_core][Thread-23] 66.67% SNPs processed. [I::csp_fetch_core][Thread-21] 66.67% SNPs processed. [I::csp_fetch_core][Thread-15] 33.33% SNPs processed. [I::csp_fetch_core][Thread-26] 66.67% SNPs processed. [I::csp_fetch_core][Thread-17] 66.67% SNPs processed. [I::csp_fetch_core][Thread-0] 25.00% SNPs processed. [I::csp_fetch_core][Thread-29] 33.33% SNPs processed. [I::csp_fetch_core][Thread-13] 33.33% SNPs processed. [I::csp_fetch_core][Thread-6] 33.33% SNPs processed. [I::csp_fetch_core][Thread-1] 75.00% SNPs processed. [I::csp_fetch_core][Thread-15] 66.67% SNPs processed. [I::csp_fetch_core][Thread-29] 66.67% SNPs processed. [I::csp_fetch_core][Thread-13] 66.67% SNPs processed. [I::csp_fetch_core][Thread-0] 50.00% SNPs processed. [I::csp_fetch_core][Thread-6] 66.67% SNPs processed. [I::csp_fetch_core][Thread-0] 75.00% SNPs processed. [I::main] All Done! [I::main] end time: 2023-02-27 11:56:27 [I::main] time spent: 1 seconds. ```

genotype.zip

[hxj5]

thanks for the detailed information. It seems the program worked well this time. The numbers of SNPs in the VCF file and three matrices are all 64, which is expected. In addition, there are some non-zero values in the AD matrix.