Hi all,
I’m using samtools calmd to add the MD tag to my bam file generated using
minimap2.
The added MD tags included lower case characters. Is this correct? According to
SAM specifications, MD should contain only upper case characters
MD:Z:[0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)*
Here, I report an example from my BAM file:
MD:Z:5^T6^C0C15A7^CT4^C1G3^C5C9^T10A24A6C5^A4^T32^T3A5A0G38^C5A1G0A4^T2^A0G10^G5A16^T1^A2^AG1C4G3^T5A2G0A8^C0G4A1G0A3G1^T5A0A0G0A0G0A4^A4A1G1G3A4^G6^G0G5A3^G5G11G2^G3C4G5G2C2T1A1^GC1G8^G0G0C4C1G0A1^G0C14A1G4^C4A8A6G1^A6A3A3^C4G9^G9A17G1C35^T2^A1G6^G5G10A3^C3A2A8t0g3g7g2g32A2^T27A1G3G1A4T2A8^A3G3A3
Many thanks in advance.
Best,
Ernesto
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