the problem of nimbus_filter.py

erasmus-center-for-biomics / Nimbus

The Nimbus software suite for the analysis of amplicon based NGS data

MIT License

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the problem of nimbus_filter.py #4

Open weibochen opened 6 years ago

weibochen commented 6 years ago

when i run the program use my datas, there is no error; but it barely detection SNVs, because most of sequences was filtered and discarded, i do not know the reasons? such as: 76M Jun 7 09:52 K1_S1_L001.discarded.bam 814 Jun 7 09:52 K1_S1_L001.passed.bam

erasmus-center-for-biomics commented 6 years ago

Dear weibochen,

without more information or examples, I can not be sure what the issue is. It could be that your reads have many mismatches or that they did not align to the amplicons. In both cases alignments would be filtered.

with kind regards,

Rutger