Hi all
I am a newbie for SAMtools, trying to find SNPs. However, SAMtools (version 0.1.18)didn't return the right result.
My command: samtools pileup -f hs_ref_GRCh37.p5_chrX.fa sub1.bam chrX > hs.txt. The result contains the information of all bases, such as:
chrX 2 N 1 ^!t I
chrX 3 N 1 a I
chrX 4 N 1 a I
chrX 5 N 1 c I
chrX 6 N 2 c^!c II
chrX 7 N 2 cc II
chrX 8 N 2 tt II
......
When I try 'mpileup' command, system warns:[main] unrecognized command 'mpileup'.
Please, I need your help.
Thanks
I am a newbie for SAMtools, trying to find SNPs. However, SAMtools (version 0.1.18)didn't return the right result.
My command: samtools pileup -f hs_ref_GRCh37.p5_chrX.fa sub1.bam chrX > hs.txt. The result contains the information of all bases, such as:
chrX 2 N 1 ^!t I
chrX 3 N 1 a I
chrX 4 N 1 a I
chrX 5 N 1 c I
chrX 6 N 2 c^!c II
chrX 7 N 2 cc II
chrX 8 N 2 tt II
......
When I try 'mpileup' command, system warns:[main] unrecognized command 'mpileup'.
Please, I need your help.
Thanks
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