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cortes-ciriano-lab / SComatic

A tool for detecting somatic variants in single cell data
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how to convert to the regular VCF file genotype such as 0/0 0/1 1/1 #15

Closed linfanxiao closed 9 months ago

linfanxiao commented 1 year ago

Dear authors,

I have been working with mouse models using scRNA-seq datasets and have obtained genotype information per cell, as shown below:

#CHROM  Start   End REF ALT_expected    Cell_type_expected  Num_cells_expected  CB  Cell_type_observed  Base_observed   Num_reads
GL456216.1  15723   15723   A   G,G Astrocyte,Neuron    19,24   ACACAGTCACGTAACT    Fibroblast  G   4
GL456216.1  15729   15729   G   A,A Astrocyte,Neuron    20,27   ACACAGTCACGTAACT    Fibroblast  A   4
GL456216.1  15909   15909   T   C,C Astrocyte,Neuron    54,44   ATGGGTTCATCCTTGC    Fibroblast  C   2
GL456216.1  34825   34825   T   A   Neuron  7   TTCGGTCTCTTTCCAA    Fibroblast  T   1
GL456216.1  34825   34825   T   A   Neuron  7   CCACCATTCGTGGAAG    Fibroblast  T   1
GL456216.1  34825   34825   T   A   Neuron  7   CGAGGCTCAGTATGAA    Fibroblast  T   1
GL456216.1  34825   34825   T   A   Neuron  7   CATCGCTCAGTCACGC    Fibroblast  T   1
GL456216.1  34825   34825   T   A   Neuron  7   TGGTGATAGTACCCTA    Fibroblast  T   1
JH584304.1  53336   53336   C   A   Neuron  4   TCCATGCGTCAGGTAG    Fibroblast  C   1

I have a couple of questions regarding this output. Firstly, I noticed that the Cell_type_expected column is supposed to indicate the specific cell-type somatic mutation, which in this example should be "Fibroblast". Should we filter out cells that do not match their expected mutation?

Secondly, I need to convert the genotype information, represented by letters such as "G" in the second line, into the regular genotype format such as "0/0", "0/1" or "1/1". This is required for lineage tracing and to generate a regular VCF4 format file for phylogenetic analysis.

Thank you for your time and I look forward to your response.

Best regards, Eric

Francesc-Muyas commented 9 months ago

Dear user, I'm sorry for not getting back to you sooner. We do not provide a tool to create a vcf file, but we have created a FAQs section to help interpret the output of this functionality.

Thanks for your patience, Fran