How to convert bam into fasta with chromosome name in fasta file having consensus sequences in fasta file

Question

[Kritika]

hi All

E00477:196:HCYTLCCXY:3:1222:9425:46542  99  A01 4   0   150M    =   157 303 AAACACGCGGATCCTTCGGGTCGGGTCGGGTCGACGCGCGGATCCCCCTTTGCTAAAACGACGCCGTTTTGTGTTTAATATAAATATAAAAAAAAGGCTAAAAACAAAACTGCTTCATCATTTTGTTGAAAAAACAGAGAGAAAACTCTC  AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJFJ  XA:Z:A10,-4883245,150M,0;D06,+59383175,150M,1;A06,+3484528,87M1I62M,3;D05,-25737025,55M1I94M,4; MC:Z:150M   MD:Z:150    RG:Z:4  NM:i:0  AS:i:150    XS:i:150   
E00477:196:HCYTLCCXY:3:2107:21105:50814 99  A01 5   0   150M    =   69  214 AACACGCGGATCCTTCGGGTCGGGTCGGGTCGACGCGCGGATCCCCCTTTGCTAAAACGACGCCGTTTTGTGTTTAATATAAATATAAAAAAAAGGCTAAAAACAAAACTGCTTCATCATTTTGTTGAAAAAACAGAGAGAAAACTCTCT  AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJFJJJ  XA:Z:A10,-4883244,150M,0;D06,+59383176,150M,1;A06,+3484529,86M1I63M,3;D05,-25737024,56M1I93M,4; MC:Z:150M   MD:Z:150    RG:Z:4  NM:i:0  AS:i:150    XS:i:150
E00477:196:HCYTLCCXY:3:1122:22648:4262  163 A01 6   0   150M    =   194 338 ACACGCGGATCCTTCGGGTCGGGTCGGGTCGACGCGCGGATCCCCCTTTGCTAAAACGGCGCCGTTTTGTGTTTAATATAAATATAAAAAAAAGGCTAAAAACAAAACTGCTTCATCATTTTGTTGAAAAAACAGAGAGAAAACTCTCTC  AAFFFJJJJJJJJJJJJJFJJJJAJJJJJJJJJJJJJJJJJJJJJJJJJJJJAFJJJJJFJFJJ<A-AJFF7<AAAFJJJJJJJJJJAJJJJJJJJJJJJFJJFFAJJJJJF<FAJJJJJJJJJJJJJJJFFJFJFJJJFJJJJJJFJJJ  XA:Z:D06,+59383177,150M,0;A10,-4883243,150M,1;A06,+3484530,85M1I64M,2;D05,-25737023,57M1I92M,3;A12,+73788594,126M1I23M,6;   MC:Z:150M   MD:Z:58A91  RG:Z:4NM:i:1    AS:i:145    XS:i:150
E00477:196:HCYTLCCXY:3:1202:19076:68816 163 A01 9   0   150M    =   124 265 CGCGGATCCTTCGGGTCGGGTCGGGTCGACGCGCGGATCCCCCTTTGCTAAAACGACGCCGTTTTGTGTTTAATATAAATATAAAAAAAAGGCTAAAAACAAAACTGATTCATCATTTTGTTGAAAAAACAGAGAGAAAACTCTCTCTTT  A-AAFFJF-<F-7AJAAFJJJJA7-A7FJ7-7-AJ<AFFFJFJJJ7JA<FA-<-<FFFJJJAJFJJFJJJJJJJF7FJAJJ-7<FJFFJFFJAJ77FJFJJJJJ-77-7AA-A7FJF-<JJJJJFFFJ<<AFAFF<<-AJJJFJFFJJFJ  XA:Z:A10,-4883240,150M,1;D06,+59383180,150M,2;A06,+3484533,82M1I67M,4;D05,-25737020,60M1I89M,4; MC:Z:150M   MD:Z:107C42 RG:Z:4  NM:i:1  AS:i:145    XS:i:145

What i want is fasta file with this format

A01 AAACACGCGGATCCTTCGGGTCGGGTCGGGTCGACGCGCGGATCCCCCTTTGCTAAAACGACGCCGTTTTGTGTTTAATATAAATATAAAAAAAAGGCTAAAAACAAAACTGCTTCATCATTTTGTTGAAAAAACAGAGAGAAAACTCTCTCTTT

[WouterDeCoster]

I'd suggest that you change the title of the thread because you are not asking for a simple conversion, rather for creating a consensus.

Answer 1

[finswimmer]

One solution with awk:

samtools view your.bam | awk -v OFS='\t' '{print ">"$3"\n"$10}'

The identifier line in fasta must start with ">". I you don't need it in your case just remove it from the print command.

fin swimmer

[Kritika]

but will it generate consensus? or it will give me each sequence with chromosome name?

[finswimmer]

No, building a consensus fasta out of bam is total diffenrent task (which I couldn't read in your initial post) than just convert bam to fasta.

[Kritika]

The fasta sequence which i listed above is

A01 AAACACGCGGATCCTTCGGGTCGGGTCGGGTCGACGCGCGGATCCCCCTTTGCTAAAACGACGCCGTTTTGTGTTTAATATAAATATAAAA

has chromosome name with all mapped cotings what i need is to convert my bam file into fasta and use it as my reference

[finswimmer]

I have the impression you are asking a XY-Question. So could you please try to explain what you realy try to solve?

fin swimmer

[GenoMax]

If you need to generate consensus sequence from your aligned BAM file follow the instructions here.