Hello everyone,
I am trying to use samtools mpileup. I am using the settings:
When I look in the output, I see this result:
This means each position has SNP, and the read base is an integer...
When looking at the input bam file, everything looks fine in IGV. Also the source looks exactly as expected:
The reference sequence looks like this (so you can see the first reference bases are found by samtools mpileup):
When looking at this data, there has something to be wrong with the bam file, does anyone know what this might be?
I am trying to use samtools mpileup. I am using the settings:
Code:
samtools mpileup -f ../chr12Ref.fa chr12.bam > chr12.vcf
Code:
SL2_40ch12 1 C 0 SL2_40ch12 2 T 0 SL2_40ch12 3 A 2 .^]. ;= SL2_40ch12 4 T 2 .. ;@ SL2_40ch12 5 A 2 .. D@ SL2_40ch12 6 G 2 .. BD SL2_40ch12 7 C 2 .. AD SL2_40ch12 8 A 3 ..^]. B?@ SL2_40ch12 9 A 3 ... DBB SL2_40ch12 10 A 4 ...^]. ?:C@
When looking at the input bam file, everything looks fine in IGV. Also the source looks exactly as expected:
Code:
@HD VN:1.3 SO:coordinate @SQ SN:SL2_40ch12 LN:65486253 @PG ID:bwa PN:bwa VN:0.7.4-r385 FCD116PACXX:8:1212:1169:72997#GTCCAGAA 117 SL2_40ch12 1 0 * = 1 0 ATGCATAGACAAGGTCTTGACGGACCTCCACAAACAAATTTGACATTTTTGATGTCAGAATCCGGATCACCCAAAAAATGCTTTGCTATAGCACACAAAA EEDEEEDDDDCDDCDDDDDDDDC?DDEDFFFFHFHHFHGIJIHFJJJIJJJJJJJJJIJHFIGIJIHGCJJJJJJJJIIIJJJJJJJHHHGHEDDFFCCB FCD116PACXX:8:1212:1169:72997#GTCCAGAA 153 SL2_40ch12 1 37 100M = 1 0 CTATAGCAAACCTTTTTTTGGGTGATTCGGATTCCGATGTCAAAAATGCCAAATTTTTTTGTGGACGCCCGTCAAGACCATGTATATGCATCCGGTTGGC EEEEDDDDC>@DBDBDDBDDDCDDB@@DDC@DDDBDC@C?BDEDDDDCEEEEEDHJJJJIIEIIGIGGIHCIJIGHFJJJJJJJIJJHHGHHFFFFFCC> XT:A:U NM:i:0 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:100 ZQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@E
Code:
>SL2_40ch12 CTATAGCAAACCTTTTTTTGGGTGATTCGGATTCCGATGTCAAAAATGCCAAATTTTTTTGTGGACGCCCGTCAAGACCA TGTATATGCATCCGGTTGGCCCTCACGGCCCGTCCGACCCATTAAGAAGGTCAAACGAGCCCCGAAGCGAGCATACCCCT CATTTCGATCATTTTCGTGTGCTATAGCAAACCATTTTTTGGGTGATCCGGATTTCGACGTCAAAAATGCCAAATTTTTT
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