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single-cell-genetics / cellsnp-lite

Efficient genotyping bi-allelic SNPs on single cells
https://cellsnp-lite.readthedocs.io
Apache License 2.0
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How to use cellsnp-lite #89

Closed DaliBAmor closed 1 year ago

DaliBAmor commented 1 year ago

Hello , I want to thank you for this fantastic tool and i would be really greateful if you can answer my question -Question 1: could we use cellsnp-lite on Human BAM file generated by cellranger count ( the fastq file are genetaed by 10* genomics using the manifacture protocole) Question 2 : could you give as an example of a command line inorder to know how to use cellsnp-lite like you did here in the case of cellsnp ( # 10x sample with cell barcodes cellSNP -s $BAM -b $BARCODE -O $OUT_DIR -p 22 --minMAF 0.1 --minCOUNT 100) Question3 : what's the tool that you created for indels detection please

thank you in advance I hope you will answer my questions

hxj5 commented 1 year ago

Hi, thanks for your interest in cellsnp-lite. Q1: yes, cellsnp-lite could be applied on 10x data generated by cellranger count. Q2: cellsnp-lite -s $BAM -b $BARCODE -O $OUT_DIR -p 22 --minMAF 0.1 --minCOUNT 100 --gzip. For details, you may look into the manual. Q3: the tool for indel detection is still under development, we may try to release the alpha version.