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Single cell snp-calling

thuthu Member
edited February 4 in Ask the GATK team

Hi,
I am dealing with some single cell data of breast cancer line. I have two questions:
1. I don't know if I need to make some changes when I do snp-calling on single cell data
2. Each sample (cell) have four uBam files. It seems that they come from different lanes, I just show the the name of first read of each file below:
Sample1.file1: HS32_13160:1:1101:3804:2200#1
Sample1.file2: HS32_13160:2:1101:5014:2219#1
Sample1.file3: HS31_13175:1:1101:2905:2214#1
Sample1.file4: HS31_13175:2:1101:2640:2225#1
However the four uBam files have the same ID value of RG tag, I just show them below:

Sample1.file1:
@RG ID:1#1 PL:ILLUMINA PU:140605_HS32_13160_A_H9FDBADXX_1#1 LB:10450847 PG:BamIndexDecoder CN:SC
@PG ID:SplitBamByReadGroup PN:SplitBamByReadGroup PP:BamMerger DS:Split a BAM file into multiple BAM files based on ReadGroup. Headers are a copy of the original file, removing @RGs where IDs match with the other ReadGroup IDs

Sample1.file2:
@RG ID:1#1 PL:ILLUMINA PU:140605_HS32_13160_A_H9FDBADXX_2#1 LB:10450847 PG:BamIndexDecoder CN:SC
@PG ID:SplitBamByReadGroup PN:SplitBamByReadGroup PP:BamMerger DS:Split a BAM file into multiple BAM files based on ReadGroup. Headers are a copy of the original file, removing @RGs where IDs match with the other ReadGroup IDs

Sample1.file3:
@RG ID:1#1 PL:ILLUMINA PU:140606_HS31_13175_B_H9FDUADXX_1#1 LB:10450847 PG:BamIndexDecoder CN:SC
@PG ID:SplitBamByReadGroup PN:SplitBamByReadGroup PP:BamMerger DS:Split a BAM file into multiple BAM files based on ReadGroup. Headers are a copy of the original file, removing @RGs where IDs match with the other ReadGroup IDs

Sample1.file4:
@RG ID:1#1 PL:ILLUMINA PU:140606_HS31_13175_B_H9FDUADXX_2#1 LB:10450847 PG:BamIndexDecoder CN:SC
@PG ID:SplitBamByReadGroup PN:SplitBamByReadGroup PP:BamMerger DS:Split a BAM file into multiple BAM files based on ReadGroup. Headers are a copy of the original file, removing @RGs where IDs match with the other ReadGroup IDs

How should I deal with these files?

Thank you!

Post edited by thu on

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