How to use `mutscan` with UMI ?

[biofer]

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！

[yanjunbiocsi]

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