How to use mutscan with UMI ? #16
Description
when use fastp + gencore , can not use GATK SamToFastq.
gencore copy the flag of R1 reads as R2 reads (or R2 as R1)?
For example，
Before gencore
A00877:990:HL5F3DSX3:4:2111:6361:29731:UMI_CCCTGAGTGT 1187 chr1 27023101 60 2S111M = 27023101 111 GCGGGAAAGGAGCTGCAGGACGGGGCCGAGAGCAATGGGGGTGGCGGCGGCGGCGGAGCCGGCAGCGGCGGCGGGCCCGGCGCGGAGCCGGACCTGAAGAACTCGAACGGGAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF: NM:i:0 MD:Z:111 MC:Z:2S111M AS:i:111 XS:i:20 RG:Z:M30713-3MJ15_M30713-3MJ15_llluma_L4
A00877:990:HL5F3DSX3:4:2111:6361:29731:UMI_CCCTGAGTGT 1107 chr1 27023101 60 2S111M = 27023101 -111 GCGGGAAAGGAGCTGCAGGACGGGGCCGAGAGCAATGGGGGTGGCGGCGGCGGCGGAGCCGGCAGCGGCGGCGGGCCCGGCGCGGAGCCGGACCTGAAGAACTCGAACGGGAA FFFFFF,FFFFF::FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF NM:i:0 MD:Z:111 MC:Z:2S111M AS:i:111 XS:i:20 RG:Z:M30713-3MJ15_M30713-3MJ15_llluma_L4
After gencore
A00877:990:HL5F3DSX3:4:2111:6361:29731:UMI_CCCTGAGTGT 1187 chr1 27023101 60 2S111M = 27023098 111 GCGGGAAAGGAGCTGCAGGACGGGGCCGAGAGCAATGGGGGTGGCGGCGGCGGCGGAGCCGGCAGCGGCGGCGGGCCCGGCGCGGAGCCGGACCTGAAGAACTCGAACGGGAA FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NM:i:0 MD:Z:12G2G17T24G8G11G1G18T1G8 MC:Z:3M1D110M AS:i:66 XS:i:22 RG:Z:M30713-3MJ15_M30713-3MJ15_llluma_L4 FR:i:3
A00877:990:HL5F3DSX3:4:2111:6361:29731:UMI_CCCTGAGTGT 1187 chr1 27023101 60 2S111M = 27023101 111 GCGGGAAAGGAGCTGCAGGACGGGGCCGAGAGCAATGGGGGTGGCGGCGGCGGCGGAGCCGGCAGCGGCGGCGGGCCCGGCGCGGAGCCGGACCTGAAGAACTCGAACGGGAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF: NM:i:0 MD:Z:111 MC:Z:2S111M AS:i:111 XS:i:20 RG:Z:M30713-3MJ15_M30713-3MJ15_llluma_L4 FR:i:3
Am I making a mistake, or is there some other solution。
I want run fastp with the ConsensusReads.
Thank you for your great work！