Entering edit mode
4.9 years ago
gokberk
▴
90
Hi all,
I'm using mpileup function on Linux (compiler: Ubuntu 4.8.4, samtools version 1.6-5-gfe1a2e9) to generate a consensus fasta using the following command:
samtools mpileup -uf human_nanogv2.fa --bam-list bam_list | bcftools call -c | vcfutils.pl vcf2fq > consensus.fa
This command creates a consensus fasta, but with some characters other than ATCG such as M, R, Y, W and S. A sample from the generated consensus sequence is below:
AAGAMACAGTCTCGGGCCGGGCGTGGTGG
CTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATYRCCTGAGGTCAGG
AGTTCGAGACCAGCCTGGSCAACAYGGTGAAACCCCCATCTCTACTAAAATACAAAAAAT
TAGCTGGGCGTGGTGGCATGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGA
ATTGCTTGAACCCGGGAGGYGGAGGTCAGTGAGCTGAGATTGCACCACTGCACTCCAGCC
TGGGCGACAGAGCGAGACTTCTGTCTCAAAAAGAAAAAAAAAGAAGATGCTTATCATGGG
CCGGGCGCAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGCGGATC
ACCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATAGTGAAACCCTGTCTCTACTAA
AAATACAAGAAAATTAGCTGGGCATGGTGGCRCGTGCCTGTAGTCCCAGCTACTTGGGAG
GCTGAGGCAGGAGAATCACTTGAACCCAGGAGGTGGAGGTTGCAGTGAGCCGAGATTGCG
CCACTGCACTCCAGCNTGGGCAACAGAGTGAGACTCTGTCTCAGAAAAAAAAAAAAAAAA
AAAAAAAAAGATGCCTATGGCCGGGCGAAGTGTCTCACACCTGTAATCCCAGCATTTTGG
GAGGCCAAGGCGGCTAGATCACTTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGG
TGAAACACTGTCTCTACTAAAAATACAAAGAATTAGCTAGGCATGGTAGCGGGTGCCTGT
AATCACACCTACTCAGGAAGCTGAGGNNNNNNNNTCTTTTTTTCTTTTTTTTTTGAGACA
GAGTTTTGCTCTTGTTGCCCAGGCTRGAGTGCARTGGCRYGATCTTGGCTCACYGCAACC
TCCRCCTCCCRGGTTCAAGTGATTCTCCTGCCTCAGCCTCCCRAGTAGCTGGGATTACAG
GCATGYGCCACCACGCCCRGCTAATTTTGTATTTTTAGTAGAGACGGGGTTTCWCCATGT
TGGYCAGGCTGGTCTYGAACTCCTGACCTCAGGTGATCCACCYRCCTCRGCCTC
I was wondering if this is an issue about mpileup and my fasta is corrupted or if these letters indicate indels etc. However, I could not find any documentation about such letters online. I would be more than happy if you could help me with this.
Best regards, Gökberk
